To Far Away Times

To Faraway Times(title needs work) ideas/outline

Picture to use for story:

http://3.bp.blogspot.com/-rvGeo4ugUv4/TvD1yzTyjhI/AAAAAAAAYn8/eo-nA0F99RU/s1600/100840+-+Artist+SilentButBeardly+Clover_the_Clever+skyrim+twilight_sparkle+winter.jpg

http://silentbutbeardly.deviantart.com/art/Of-Sparkles-and-Spell-Tomes-274767579?

Possible alternate picture:

http://1.bp.blogspot.com/-ItBpyi58-H8/TvTxWedleFI/AAAAAAAAZBg/o81o2tApK30/s1600/102798+-+applejack+apple_bloom+artist+imdrunkontea+book+fluttershy+mane_six+night+pinkie_pie+rainbow_dash+rarity+scootaloo+shooting_stars+spike+stargazing+Sweetie_Belle+telescope+twilight_sparkle.jpg

http://imdrunkontea.deviantart.com/art/MLP-Stargazing-275426973



The basic idea behind this story is to take the essential story elements of Chrono Trigger--a Lavos-like entity, time travel, worldwide destruction, and so on--and craft a story based upon those elements in such a way as to avoid both writing a cut and paste version of the source material--which would be boring--and to put a pony-like spin on the whole affair. The story will be crafted based upon all the knowledge of the history of Equestria available in the show as well as a good portion of my own fanon, due to the nature of Equestrian history being so vague in the show.

HISTORY OF THE WORLD OF EQUESTRIA(ORIGINAL TIMELINE)

Prehistoric Age: 3,000,000 B.E. In this time period in history, an ancient society of Dragons, the Dragonkin, had been exterminated by the coming of Chaos ten thousand years before. What few Dragonkin remained have fallen into barbarism, more like animals than people, occupying the few dead ruins of their civilization. When Chaos fell, a splinter of the being became a mysterious object, the Shard of Mystery, with the power to alter life in chaotic ways. Though uncontrolled by Chaos, the being is able to speak through the Shard of Mystery, and will make use of the Shard of Mystery throughout time to influence. The ancestor of modern ponies encountered the Shard of Mystery, accelerating their evolution and eventually granting them powers. This ancestor would go on to evolve into the Earth Pony, Unicorn, and Pegasi races, but this evolution would take over two and a half million years. Chaos's presence would eventually lead to the planet becoming unstable, its rotation affected and the weather, especially in what would eventually become the continent of Equestria, running out of control, needing to be controlled by intelligent beings. This is a process intentionally engendered by Chaos to force evolution along certain paths, to make for a better source of energy for its spawn.

Age of Atlantium: 20,000 B.E.: This time period is that of the first true Pony civilization, as well as a time period where Griffons reign. The shining jewel of a massive Pony empire is Mare Atlantium, a massive city that rests just beneath the waves, far away from the Griffons that rule the land. Mare Atlantium is a mecca of arcane creations, a paganistic society that worships the Sun and the Moon as well as many spirits of the sea. Massively accelerated in development due to the accidental creation of the first Alicorn by exposure to the Shard of Mystery, Mare Atlantium has set itself on a course towards destruction, a course encouraged by Chaos as it saw Mare Atlantium as a significant threat, especially due to their research into many subjects, including time travel. Ruled by Queen Unity, a cruel and terrible Alicorn, the source of their power is the Sun Stone, an artifact originally crafted by a Dragonkin. Queen Unity sought to replace the Sun Stone by channeling the very power of Chaos himself, referring to Chaos as a new God beneath the waves. This attempt would fail, and the ensuing destruction of Mare Atlantium would not only set Pony civilization back many thousands of years, but it would also set back other civilizations of sentient species across the world. Princess Cadence, the daughter of Queen Unity was saved through the use of an experimental time travel device that would strand her in the Paleopony Era.

Paleopony Era: 100 B.E : This time period is one of strife. Various Pony nations have fought over the continent of Equestria for a long period of time, but they seek to end the conflict by unifying Equestria under a coalitionary banner, uniting to oppose forces from those such as the Griffons that rule the mountains. This is the time period of Starswirl the Bearded, the creator of the Portals and the Elements of Harmony. Through the knowledge he gained from Princess Cadence, Starswirl the Bearded became aware of the existence of Chaos, and he sought to create the Elements of Harmony as a weapon with which to enable Ponies to fight against Chaos. He gathered together six souls that exemplified the virtues of Honesty, Generosity, Kindness, Loyalty, Laughter, and Love, and, with the help of Princess Cadence, converted the power of their virtues into the Elements of Harmony. He also recreated much of the research on time travel from Mare Atlantium, and created with it an Gateway that would create many Portals in time that could be used to travel throughout various eras both in the past and in the future from his current date. Unfortunately in an accident he banished himself into the End of Time, an extradimensional space that rests where time ends. This accident also sent Princess Cadence further forward in time with their foals, Celestia and Luna.  Although time passes for him at the EoT and he can observe all of history, he is trapped. The Elements of Harmony became lost in the shrine above his home, where they would not be used for several centuries.

Disharmonic Era: 475 Y.E. This is the time period where Discord came to be, a time period where Equestria has been suffering in its inability to truly unify as a central state. Discord was but a Prince in one of the many statelets that made up Equestria, living near the border with the Griffon Kingdoms. He discovered the Shard of Mystery entirely by accident, and it transformed him, much as it had transformed Queen Unity. Unlike Queen Unity, however, Discord was twisted into a Draconeqqus, a truly horrible creature with a warped mind, intentionally made by Chaos to serve as a check on the power of the Ponies as Chaos feared that Equestria would eventually become as powerful as Mare Atlantium. Discord took over much of Equestria and began using illusions and trickery to make the Equestrians believe he was a god. The reign of Discord would cause a civil war between his forces and those of the children of Princess Cadence, Celestia and Luna. Princess Cadence had been sent into this period of time after the disaster with Starswirl the Bearded that catapulted him to the End of Time; she died on the journey, leaving only her two young foals to fend for themselves. Celestia and Luna were approximately thirty years old when Discord took control of Equestria, and like their mother, they were very powerful and long lived, but not immortal. They struggled against Discord for many years, before discovering the Elements of Harmony and using them to seal Discord in stone. Chaos saw the power of the Elements of Harmony and was truly afraid, so he sought to prevent them from ever being used again by encouraging envy and hatred within Princess Luna that would eventually transform her into Nightmare Moon twenty-five years later. The Elements of Harmony were laid to rest where they had been found and the Princesses took over Equestria, unifying it as a central state under their authority, especially through the use of their magic to ensure that the Earth continued to turn.

Present Era: 1501 Y.E. This is the time period of Twilight Sparkle and her friends, the first in a thousand years to become capable of using the Elements of Harmony. Equestria has been at peace since Princess Celestia unified it, with the sheer power of her magical abilities being enough to ward off attacks from outside powers, including the Griffons. It is in the June of  1501 that Twilight Sparkle will discover Starswirl the Bearded's old research laboratory and accidentally activate the Gateway that will create the portals and scatter her friends throughout time in a manner that Starswirl the Bearded could not have predicted.

Dead Future: 2300 Y.E. This time period is one where Chaos Has Won. Twilight Sparkle and her friends were the only ones ever able to use the Elements of Harmony, and in the original timeline they died centuries before Chaos was finally ready to create his spawn. Without the Elements of Harmony and without the foreknowledge of Chaos' existence, the world was destroyed, all civilization perishing. A few remnants of populations still live here and there, on a dying world only kept rotating by the remaining power of Chaos to ensure its spawn can survive long enough to go to other worlds and repeat the endless cycle of parasitic annihilation.

HISTORY OF THE WORLD OF EQUESTRIA, ALTERED TIMELINE PRIOR TO TWILIGHT SPARKLE'S TRAVELS

Prehistoric Age: 3,000,000 B.E. This Era is not truly changed at all by the introduction of the Mane Six and the Elements of Harmony throughout time. Fluttershy was deposited in this era, and became the leader of one tribe of prehistoric pony ancestors, worshipped due to her wings. She attempts to spread a philosophy of Kindness, but her attempts will not last long after her death.

Age of Atlantium: 20,000 B.E. This Era has seen many changes, primarily in the power structure of Mare Atlantium. The Cutie Mark Crusaders were deposited in this era. They became friends of Princess Cadence and worked to become a team of researchers and creators, sticking together as close friends, encouraging the time travel research that led to Princess Cadence eventually being sent to the Paleopony Era. Unfortunately they would perish in the destruction of Mare Atlantium.

Paleopony Era:  100 B.E. The alterations to the timeline become far more grievous in this era, as due to Pinkie Pie arriving through time, Starswirl the Bearded's former assistant, Clover the Clever, was killed in the process of saving Pinkie Pie's life. Pinkie Pie became Starswirl's new assistant, but the damage was done--without Clover the Clever, the dreamstone necessary to create the Elements of Harmony would never be located, and the Elements would never be created. Instead, Starswirl contended himself with the last few years of his life by researching Pinkie's Pinkie Sense and leaving a record about Chaos that would hopefully be used by Princess Cadence to eventually have somepony else create the Elements of Harmony. Unfortunately the research and Pinkie Pie would both be lost in an attack on Starswirl the Bearded's home shortly after Starswirl's natural death, and nopony would ever be able to create the Elements of Harmony or the Portals.

Disharmonic Age: 475 Y.E. Without the Elements of Harmony, the Sisters would not be able to seal Discord in stone. Instead the war fought was far more vicious and blood-filled, a devestating war that would destroy the foundations of Equestria itself. Rainbow Dash found herself in this era, caught up in the bloodshed, eager to help Princess Celestia by becoming a Paladin in her service. Despite Rainbow's ability to perform Sonic Rainbooms, she was just one pony, and she would eventually perish in the final battle between the forces of the Sisters and the forces of Discord. During this battle the Sisters and Discord would also perish, destroying each other in one massive climatic battle that rendered Canterlot uninhabitable for centuries. Without the Sisters to unify Equestria, the nation would dissolve into warring factions, balkanizing beyond hope.

Present Era: 1501 Y.E. With the collapse of Equestria as a nation over a thousand years prior to the current date, the political situation is tumultuous. Ponyville is the capital of a small Earth Pony city state caught between the Pegasi Cloud City of Cloudsdayle and the Unicorn Kingdom of Canterlot, under seige not only from its fellow Ponies, but from a nearby kingdom of Griffons as well. Rarity was deposited fifteen years prior to the current date in the Duchy of Trottingham, a small outcropping of the Kingdom of Canterlot. Becoming a close friend and advisor of the Duke, when he died three years later she became the new Duchess, a move that made her a political enemy of many. Her reign over the next twelve years would be frought with assassination attempts on her life and her own usage of charisma and generosity to try and win peace with her neighbors. Eventually her life would be ended by a successful assassination attempt--the assassin did not survive as Rarity herself managed to strike an equally mortal blow upon the assassin.

Dead Future: 2300 Y.E. There is little different in this era from the previous timeline. Although warfare and strife had brought with it in some ways much more advanced technology, there was never a chance that the ponies could successfully prevent Chaos from destroying the world, not without the Elements of Harmony, Elements that nopony in what had become of Equestria deserved to use.  Applejack arrived in this era approximately six years prior to the current date, stuck in the EverFree forest. Though she escaped, it was not without great harm, and she would have to be nursed back to health.

PREMISE OF THE STORY:

The basic premise is that, entirely by accident, Twilight Sparkle and her friends get themselves wrapped up in a time traveling adventure that will see them changed forever, suffering in many ways until they eventually succeed in defeating Chaos. While the world will never be the same afterwards and they will never be able to return to their lives from before, their efforts will have secured them a place in history far beyond their wildest dreams.

OUTLINE OF THE STORY:

PART ONE, WHERE TWILIGHT IS CONFRONTED BY THE MYSTERIES OF TIME TRAVEL AND MUST FIND OUT WHAT IS GOING ON:

Twilight decides to do some research on the Elements of Harmony--where they come from, why they exist, etc, questions Princess Celestia does not have the answer to. Gathering together her friends, they head for the shrine in the Everfree Forest where the Elements of Harmony were first found--the CMCs come along as well. They find, beneath the shirne, an ancient arcane laboratory and living quarters, the home of Starswirl the Bearded. During their explorations of the home, the CMCs accidentally find and set off the Portal Creator, only they accidentally made it unstable because they didn't know how it worked. Twilight attempted to use the Gate Key rod--found by Rarity during their explorations--and the Elements of Harmony to stabilize the Gate, only to instead send her friends and the Elements of Harmony hurtling through time, initiating the Altered Timeline.

In the Present, Twilight and Spike find themselves in a version of the home without the Portal Creator or any evidence it was even there to begin with. After attempting and failing to either find any aid in the library, or to contact Princess Celestia, Twilight and Spike decide to return to Ponyville. They find a vastly different Ponyville, one that Twilight realizes will most likely forbid entry to a Unicorn, especially one with a Baby Dragon along for the ride. She uses her magic to disguise both herself and Spike and they gain access to the town, heading for the library to try and find information on history. They obtain a basic book on The Rise and Fall of Equestria that informs them about how Equestria no longer exists. They also encounter in Ponyville a Gate, located in the town square. After deciding they have no real choice in the matter, they enter the Gate, heading to the Disharmonic Era.

In Disharmonic, they arrive in a clearing in a forest, as Ponyville would not be founded for several centuries. In an attempt to figure out when in time they are, they head for a nearby road, and run into a party of monsters being led by an insane Unicorn, a Worshipper of Discord. They attempt to fight, but are no match--before Twilight and Spike are killed, Rainbow Dash swoops in to save them, defeating all the monsters herself. She then gets Twilight and Spike to follow her because it is extremely dangerous to be so close to Canterlot, where Discord reigns from. They escape to Starswirl's home in the Everfree Forest, which has been converted into a safehouse for the forces of Celestia and Luna, hidden from Discord due to the chaotic nature of the forest. There, they rest for the night while Twilight and Rainbow Dash confer on what has happened. Rainbow Dash is a Paladin in Celestia's service. They decide to seek Celestia's help. Over several days they travel to meet Celestia in Hoofington, one of the centers of the resistance against Discord. They are forced to wait for several more days for Celestia to arrive--during this time Rainbow Dash sees to it that Spike and Twilight receive some significant martial training, to prepare them for fights. When they meet Celestia, they find out that Celestia herself has traveled through time, though only as a foal, and that she has no idea what is going on, and that she has no idea what the Elements of Harmony are as she's never heard of them, and they are of course not present in the shrine. Twilight is even more confused, but asks Celestia's permission to take Rainbow Dash with her to travle through time to try and figure out what is going on. With Celestia's blessing, they head for a nearby Gate. Unfortunately they are spotted by forces of Discord, requiring them to avoid returning through the Gate for some time. The Gate leads them to the Dead Future.

In the Dead Future, they are shocked and horrified to discover what has happened to Equestria, now far more confused than ever before. They make their way from the ruins of Hoofington to the ruins of Ponyville, fighting monsters and horrible mutated beasts along the way, as well as the occasional robot. When they make it to Ponyville, they find the Dead Future Survivors, Applejack among them. Applejack tells them her story and that she doesn't know what's going on, but she DOES know how they can find out, and along the way they can perform a significant service for her fellow Survivors. Deep within Ponyville they find a military complex, where the security system has gone absolutely nuts, trying to kill anypony that so much as comes near the place. Within they will find replacement parts and other goodies for the Survivors as well as a massive military database, complete with an Apocolyptic Log about the Chaos that overtook the world. After absorbing the information, they decide that not only will they fix history, but they'll stop this Chaos thing too: it's their duty, after all, as the Elements of Harmony. Using a spell, they find two other Gates they can use to travel in time--one in the devestated ruins of Canterlot and one near Trottingham, several days walk away. They decide to use the Trottingham gate because they don't want to accidentally end up in Discord's lap in Canterlot, something that would end in a quick death for them. After some finangling they find the Ponyville Aerodrome and force a vehicle of some sort(airship? Balloon? Some kind of plane?) to work in order to significantly cut down on travel time to Trottingham, though they're attacked on the way by flying mutants of some sort. (Griffons?) They go through the Gate, but because there are four individuals, the Gate malfunctions. Instead of being scattered throughout time, they are brought to the End of Time by Starswirl the Bearded. (END PART ONE)

PART TWO WHERE TWILIGHT MUST FIND AND RECOVER HER FRIENDS FROM TIME:

In the End of Time, Starswirl the Bearded confronts Twilight and her friends about her actions, the damage she's done to history, how disruptive every moment she was in the past already has been to his picture of the timeline. He lectures them, talking about how one cannot simply waltz through time and expect everything to be exactly the same when they return to the future from the past. The butterfly effect and all that. After his lecture he softens and chides himself for attacking the single best hope the world has for saving it from Chaos. He explains how he created the Gates and the Elements of Harmony to fight Chaos, and how they must work together to become strong enough to defeat Chaos. He knows they must achieve three significant tasks: First, they must continue to recover Twilight's friends from time, so as to gather together the Six Bearers of the Elements of Harmony. Second, they must retrieve the Elements of Harmony themselves from history, in order to take back control of what is theirs. Third, they must go throughout history and fix the damage they've done, to try and recreate at least an approximation of the peaceful Equestria they knew and loved before this all began, so they have something they want to return to. These tasks will help strengthen them for their final task: Defeating Chaos. Unfortunately Starswirl's explanation is interrupted, as he suddenly realizes they have little time to act, because Rarity in the Present is about to suffer the successful assassination attempt that will not only end her life, but that will also destroy any chance of defeating Chaos. Twilight, Rainbow Dash, and Applejack hurry to the Present, leaving Spike behind. (Does Starswirl also give them the two-way radio/teleporter device now? Not sure.)

In the Present, they arrive near Trottingham and race to the Duchal Palace at the center of the city, where they manage to reach Rarity just in time to save her from a magically cloaked assailant. The unicorn that attempted to kill her is beaten into unconsciousness by Rarity and escorted to the dungeons to be interrogated and then hanged for his crime. They are happy to see Rarity, and Rarity is especially happy to see them--she sees to it they're given royal treatment, and over dinner and so on she explains to them what has happened, while they explain to her in turn what is going on and why they need her to come with them. Rarity is reluctant...on the one hand she can see their point, but on the other hand she doesn't want to just abandon her subjects. Twilight points out that, if they succeed, her subjects wouldn't even exist anyway. If they fail, there won't be much point to leading ponies anyway since they're all doomed. Rarity takes the night to think on it and agrees the next morning, ready to head out, taking full advantage of her position as royalty to secure them much needed supplies and to give them better weapons and armor. (Except for Applejack, whose scavanged weaponry from the robots in the Future cannot be duplicated. Fortunately Applejack has plentiful ammunition and does not always need to use it, resorting to her hooves in many fights, and if they really need to they could probably scavange plenty in the ruins of Trottingham in the Dead Future.) The amount of supplies they receive is not only for them personally, but to supply the party at the End of Time over several weeks at a minimum. Before they return to the End of Time, Twilight uses her Gate finding spell to see if any other gates are in the Present--as it turns out, one is located to the north of Ponyville, near the base of Canterlot Mountain. They then return to the End of TIme and inform Starswirl they will be heading for the Canterlot Gate. Rarity goes along with Twilight, as does Spike. The journey is uneventful?

When they reach the Gate, they enter it and are returned to the End of Time where two new Gates are now accessible. Starswirl the Bearded informs them that the Gate will take them to the Paleopony Period, where they will encounter both their friend Pinkie Pie and his younger self, a stallion changed by time travel. Starswirl tells them that they must aid his younger self in completing the Elements of Harmony, but that under no circumstances are they to inform him that they are time travelers. He does not want to risk his younger self time traveling and causing massive issues. So long as they do not inform the younger Starswirl that they are time travelers, the Elements of Harmony will be completed and the time duplicate Starswirl as well as the duplicates of Princess Cadence and the Sisters will vanish when they reach the point in time in which they originally time traveled, as he has confirmed through his observations. They must tread very carefully, and Spike cannot accompany them as a Baby Dragon familiar would be extremely suspicious, nor can Applejack come along due to her weaponry being....historically inaccurate. Thus, Rarity and Rainbow Dash accompany Twilight to the Paleopony Period.

In the Paleopony Period, they encounter Pinkie Pie in the town at the base of Canterlot Mountain, where she is attempting to find a source of Dreamstone. Naturally ecstatic to see them, she makes them come along with her to her home with Starswirl the Bearded and the Alicorns, telling them along the way about her new life and being informed about the mission they are on, which Pinkie Pie is of course ready to help them with! (They don't explain to her that her new friends will disappear, at least not yet.) When they arrive, it doesn't take too long for Pinkie to convince Starswirl that her friends(old friends she's rediscovered!) can help them with their Dreamstone problem, and that she has to go with them. They say they will return as soon as possible. They leave with Pinkie Pie to return to the End of Time, where they then take the Trottingham Gate to the Dead Future. Spike comes along, as does Pinkie Pie.

In the Dead Future, it doesn't take them too long to head for the Canterlot Gate, which they now know will take them into the distant past. Pinkie is confronted by the realities of the Dead Future and is very upset--the journey to the Canterlot Gate is filled with her remnisicing with Twilight and the two forming a new bond. When they reach the Canterlot Gate, they confirm through Starswirl at the End of Time that it leads to 3,000,000 B.E, where they will find Fluttershy, whom they're all really happy to be able to see. Starswirl has no idea where they'll find the Dreamstone, of course, but he knows there should be plenty in the era, and so they head to the Prehistoric Era.

In the Prehistoric Age, Pinkie Pie, Twilight, and Spike soon come across Fluttershy in a fight for her life against some Dragonkin. Though they try to help, their help isn't needed: Fluttershy takes down all the Dragonkin, without killing any of them of course. She almost takes down Spike before she realizes who he is, and when she does realize who they are, she's so happy she can barely contain herself. For their part they're pretty proud of Fluttershy's abilities. Fluttershy tells them to come with her to the village of Prehistoric Ponies, though she says that Spike can't come along and that Twilight should hide her horn, so Spike switches with Applejack. While Fluttershy is very confused by this, since they haven't been able to explain anything yet, the explanations are held off till they get to the village. The village is full of Prehistoric Ponies, which are closer in appearance to real-world ponies: no binocular vision, bulkier, longer muzzles, etc. The Prehistoric Ponies hold a celebration for them in their honor, where Fluttershy explains they've been revering her almost like a Goddess because of her wings, and she's been trying to protect them. However, because they are so child-like--the most intelligent of them is like a five year old child at this point--she's been extremely lonely, and she is rather upset when Twilight explains what all has been going on. Despite that, Fluttershy doesn't need much encouragement to join them in their quest, saying she may have seen something like what they need in a nearby ruin, occupied by Dragonkin. They get ready to set out the next day.

In the Prehistoric Age, Fluttershy leads Twilight, Pinkie Pie, and Applejack to the ruin, where they find a settlement of Dragonkin. In exploring the ruin, they eventually come upon a large bounty of Dreamstone, apparently harvested for use by the Dragonkin but never put to use due to the destruction of their civilization. They also discover the first Element of Harmony to be found, the Element of Kindness, though it is protected by the Dragonkin and they are forced to fight off a major force of them to obtain it. With it and the Dreamstone, they are able to return to the End of Time.

At the End of Time, Fluttershy takes a much needed break, so she can catch up with her other friends. The bounty of Dreamstone is more than enough for the creation of the Elements of Harmony--enough even to create a more powerful Gate Key that can stabilize the Gates so they can take seven individuals through time at once, allowing everyone to travel together.

They return to the Paleopony Period, Twilight accompanied by Pinkie Pie and Rarity. Unfortunately, when they arrive, they discover that Princess Cadence had figured out they were time travelers, prompting a very long and powerful discussion. Starswirl the Bearded at the End of Time is forced to tell his younger self what will happen to them and how he musn't interfere, but must still create the Elements of Harmony to ensure his children have a future. Pinkie Pie is equally shocked as she didn't understand that this was going to happen. While Starswirl the Bearded prepares the ceremony that will create the Elements, Princess Cadence takes Twilight and friends aside and tells them more about Mare Atlantium, including about the Cutie Mark Crusaders and how they tried to stop the usage of the Element of Magic and were captured and executed by drowning as a result. Rarity--and Applejack, and Rainbow Dash, overhearing through the radio--are all heartbroken, but Twilight is able to recover enough to ask for the date, figuring out that it wouldn't happen for another few weeks and that, if they can gain access to the Age of Atlantium, they might be able to save the CMC's lives AND get the Element of Magic in one fell swoop, which makes everypony a little happier and more determined than ever. Starswirl asks them to rest for the night; the ritual will be performed tomorrow. During the night, Twilight sends Spike back with the Gate Key so that Fluttershy, Rarity, and Rainbow Dash may come along to help with the ceremony.

The ceremony proceeds the next day, with everypony assisting. After the Elements of Harmony are created, they are aligned with the young Celestia and Luna so that their future selves may use them in the Disharmonic Era. Starswirl the Bearded at the End of Time informs them that his younger self, Princess Cadence, and the two Sisters will soon vanish, and Pinkie Pie insists they stay with them till the end. Twilight sends everypony else ahead and stays with Pinkie. Pinkie gathers her adopted family around her and holds them until they vanish in an instant without warning. Though Pinkie is extremely saddened, Twilight does her best to comfort her, forming closer bonds.

END PART TWO

PART THREE WHERE TWILIGHT AND FRIENDS MUST LOCATE AND RECOVER THE ELEMENTS OF HARMONY:

When everypony returns to the End of Time, they discover that Starswirl the Bearded has managed to locate the Elements of Harmony. The Element of Loyalty is in the Disharmonic Era, hidden within a fort manned by Worshippers of Discord, halfway between Canterlot and Trottingham, held due to its obvious magical nature, having been found but not identified. It will eventually be transferred to Discord's treasury in Canterlot, but until after the battle between Discord and the Sisters(a battle that, for now, still ends in their deaths even WITH the Elements of Harmony, something Twilight and friends have decided they need to correct, but they are not yet ready to do.) The Element of Honesty is in the ruins of Manehatten in the Dead Future, where it has been hooked up for the past twenty years to a computer A.I. attempting to use its power to bolster its army of robots. The A.I. is insane, naturally, and the robots are numerous. It will require their full efforts to take them down. The Element of Generosity is in the Present, in an underground church in Ponyville, being used as a sacred item for those who worship Celestia and Luna as Goddesses who saved everypony from Discord, a practice banned by the government of Hoofington and its subordinate state in Ponyville. The Element of Laughter is...somewhere in the Paleopony Period, inside Hoofington, possibly on the streets being sold as jewelery.  The Element of Magic is, of course, in Mare Atlantium, which they are still unable to reach. Starswirl says he believes there is a portal in Canterlot Castle in the Disharmonic Era that may lead to the Age of Atlantium, but he is unable to be sure as Discord's presence makes it difficult for him to determine. He says he will keep trying to see, and that he will also attempt to gather more intelligence on Mare Atlantium, though like with Discord the magic of Mare Atlantium makes observing the period very difficult.

Twilight decides they will seek the Element of Generosity first, so they can gain access to the Gate in Ponyville to make it easier to get close to Canterlot in the Disharmonic Era, as well as get closer to the fort with the Element of Loyalty. She asks that the others spend some time training, and takes Rarity alone with her to the Present. She and Rarity disguise themselves as Earth Ponies and enter Ponyville, seeking out the librarian that helped Twilight before, as Twilight suspects the librarian may be part of the Church of the Sisters. In reaching the librarian, they manage to convince her they worship Celestia, particularly by showing that they're disguised unicorns. The librarian, who is TRIXIE, agrees to help them and they attend a service, after which they speak with the leader of the church and explain why they need the Element of Generosity, that they can put it to use to prevent Celestia's death in the first place. Rarity manages to be charming enough to convince the leader, and they succeed in getting the Element. Unfortunately, as they are leaving, they are caught by soldiers who were raiding the church, forcing Rarity  and Twilight to fight their way out. A number of Sister worshippers die in the process, including Trixie, to Twilight and Rarity's dismay, but they manage to get away and escape through the Gate in Ponyville Square, returning successfully to the End of Time, and holding a small moment of silence for those lost. Starswirl reassures them that they can still change the Present to something more like what they're used to, which reassures them.

The Element of Loyalty is next. Twilight decides they will need help with this assault, and so they seek out the forces of Celestia and Luna to see if they can't help. While they can't help assault the fort itself, they can distract the fort with a small army from Trottingham, drawing out most of the forts soldiers. They will also set up an extraction point to help Twilight and friends escape when needed. Twilight sends Rainbow Dash and Fluttershy ahead to scout out the fort and figure out the best way in, while the rest of them make a slow walk to close to the fort. The Pegasi return and say that the fort is actually undermanned--they witnessed a number of its forces leaving for Trottingham. What's left are mostly monsters and not that many actual pony troops. The fort itself is halfway buried inside a hill, making an assault difficult. Twilight decides the best way to assault is with a two-pronged attack, with Rainbow Dash carrying Applejack in from above under an illusion cast by Twilight so they can get close enough to avoid the crossbows--once down, Applejack's weaponry will be more than enough to take down the other guards in the area, giving Rainbow Dash and Fluttershy a chance to ferry in Rarity, Twilight, Pinkie Pie, and Spike. Naturally, the plan goes sour--Rainbow Dash and Applejack are injured on the flight, and though they manage to take out a number of guards, they're captured. Twilight mounts a rescue by teleporting in with Spike and distracting the monsters long enough to let Pinkie Pie and Rarity break in through the front gate. Though the battle leaves several of our heroes injured, it is ultimately a success, as they are able to find and obtain the Element of Loyalty, though not until after a massive battle with the leader of the fort. Twilight and friends make their escape to the extraction point, where they successfully get away to heal their wounds, needing a day or two for recovery.

The Element of Honesty is next, deep within the ruins of Manehatten, kept in a military outpost. Though the robots are everywhere, they are not very intelligent, particularly not when commanded by an insane A.I.. Twilight and friends battle their way through the ruins, destroying countless robots of various kinds before they finally reach the military outpost itself, which has automated turrets and other heavy defenses that make getting in quite tough. Applejack manages to rig up a missile launcher from a fallen robot to take out the turrets, and they break in. Few robots are left inside the base, as most were destroyed outside. When they reach the A.I., they find out it was programmed by relatives of the Apple Family, and that it was actually the leftover personality of a distant Apple descendant that had merged with the computer. Applejack is rather saddened by that, but together she and her friends destroy the A.I. and retrieve the Element of Honesty.

For the Element of Laughter, they arrive in Hoofington and begin tracking down the necklace. They soon find it has been changing hands repeatedly, being sold and resold and resold, until they finally manage to track it down, having been given as a gift to a lonely, homeless foal. Pinkie takes the time to do her best to cheer up the foal, and they give the foal as much money as they can in exchange for the Element of Laughter.

With five out of six Elements of Harmony gathered, all that is left is the Element of Magic. By now, Starswirl the Bearded has confirmed that the Gate to the Age of Atlantium is in Canterlot in the Disharmonic Era, and that, without their assistance, the Sisters will still die in the coming battle. In order to save the Sisters and allow them to properly use their own Elements of Harmony against Discord, they must first remove Discord's source of power, the Shard of Mystery, which they should retrieve so that Starswirl the Bearded may study it and hopefully gain some better insights into the nature of Chaos, though he warns they must be extremely careful with it, as it could potentially affect them as it did Discord and Queen Unity. Twilight and friends make their way to the Disharmonic Era, where they return to Hoofington to speak with the Sisters, whom they convince to prepare for their final battle. The plan is this: Rainbow Dash will lead Applejack, Spike, Rarity, and Fluttershy who will stand by while Celestia's forces prepare for battle. Meanwhile, Twilight and Pinkie Pie will sneak in through hidden tunnels in Canterlot Castle that not even Discord is aware of and inside--Twilight because of her magic, and Pinkie Pie because her Pinkie Sense is too useful a tool to leave her behind. Once inside, they will retrieve the Shard of Mystery and make their escape. If they need help, the rest of the Mane Six will give it to them. Celestia and Luna agree to the plan.

Twilight and Pinkie Pie make their way to the entrance to the tunnels as per the plan, and then wait until nightfall inside a cave nearby, cuddling together for warmth. (This should be a touching moment. Maybe admit feelings towards each other? Or at least subtly show that there are feelings there.) When night falls, they sneak in through the tunnels. Though confronted by several Worshippers, Pinkie Pie pulls off an incredible performance that is more than enough to convince the worshippers that Twilight and Pinkie are also worshippers. With that, they're able to proceed with less need for care, till they find out the Shard of Mystery is kept in the vault. They make their way there, and confront a significant problem: a number of guards that seem very reluctant to let them even get near the Vault, let alone get inside. Twilight and Pinkie discuss the issue and Twilight finally decides she'll chance charming the guards with the love it spell. It causes the guards to go a little nuts fighting over an object, but it gives Twilight and Pinkie the chance to sneak and get the Shard of Mystery. The Shard of Mystery, being a conduit to Chaos, attempts to toy with their heads, but the preparations they made to ward it off are successful at keeping either of them from going insane or being affected by its power. (Though Twilight is for a moment tempted to indulge in the use of it, she manages to fight off the impulse.) They escape into the tunnels and succeed at getting away, fleeing as fast as they possibly can till they reach Rainbow Dash and Fluttershy. Fluttershy takes the Shard of Mystery and flies for all she's worth to reach the Gate. Discord has realized what is going on and started chasing after Fluttershy, but he is unable to reach her in time. Twilight, Pinkie, and Rainbow Dash rejoin the others and the battle begins in earnest, with lots of hard fought action as Celestia and Luna's forces advance on Canterlot, while Discord himself battles with the Sisters in the sky. Finally the Sisters are able to use the Elements of Harmony to lock Discord in stone--because they were in the air when this happened, the statue falls and shatters, eliminating Discord permanently. The Sisters further use the Elements of Harmony to banish as much of Discord's magic as they can, restoring Canterlot to a beautiful place as well as clearing the minds of most of Discord's worshippers. Without Discord to keep them going, most of the monsters perish--the ones that don't are quickly eliminated. With the day saved, Twilight and her companions enter the Gate, now easily found in the Canterlot Throne Room, returning to the End of Time to rest after the long and wearying battle.

Unfortunately, as they learn when they arrive at the End of Time, there is little time to rest. With access to the Gate, Starswirl the Beard's ability to look into the timestream in the Age of Atlantium is much clearer, and he has realized that they had miscalculated the dates given to them by Princess Cadence--Mare Atlantium is preparing to execute the CMCs in just a few hours, and begin the experiment that would destroy it not an hour later. They have very little time to figure out how to get into the city and save the CMCs. Starswirl the Bearded gives them what information he can, writing down a method he saw to get into the city so they can access it, as well as giving them cloaks he had prepared some time ago with spells on them that cause those looking upon them to disregard them--the spell is not very strong as, if it were, it would alert unicorns, but it is just strong enough that, so long as they do not act suspiciously, no one will see them as odd. Despite their weariness, they make their way through the gate to the Age of Atlantium, agreeing ahead of time that if they have to fight, there will be no mercy shown: after all, everypony in Mare Atlantium will be dead in a few hours anyway, so there is no reason to hold back.

The Gate drops them off on a cliff overlooking the ocean. Not too far away is a building with the symbol of Mare Atlantium upon it, exactly what they are looking for. They go inside and use the spell Starswirl taught them to access the city. Inside, as they expected, no one pays them any mind--they take care to walk the city carefully. It is massive, with many thousands upon thousands of ponies, making Twilight very sad that they are all about to die in a few hours and there's nothing she can do about it. As time slowly ticks down, they start to panic about ever finding the CMCs...eventually Twilight decides to ask a guard about political prisoners. The guard happily informs them that three traitors are being executed within the next few minutes at a location not too far away, and if they hurry they can see it! This causes everyone to make a mad dash for the place in question--they arrive just as the CMCs are being placed underwater. With no time to lose, they take down the guards and release the CMCs, saving their lives! The crowd panics--a few try to attack the party and are swiftly cut down, while the rest flee, except for Princess Cadence. Rainbow Dash, Applejack, and Rarity have a very touching reunion with Scootaloo, Apple Bloom, and Sweetie Belle respectively. ("I guess I'm the big sister now, huh?") Unfortunately, because of the panicking crowd, they are now wanted, though Princess Cadence, realizing they are trying to stop her mother, does her best to keep the guards distracted. Twilight orders Rainbow Dash, Rarity, Applejack, and Fluttershy to escort the CMCs back to the Gate, saying she, Pinkie Pie, and Spike will make their way down below on their own--they briefly stop by the CMCs hidden laboratory to obtain a device that was meant to be used to sabotage the experiment and make the Element of Magic able to be removed. With the aid of Princess Cadence's distractions and help in finding their way(and in knowing there's an escape method available to them at the bottom that will teleport them to near the Gate's location), as well as Pinkie's Pinkie Sense, Twilight, Spike, and Pinkie are able to make their way to the bottom and reach Queen Unity and the Demon Machine, only fighting a few guards on the way.

Barely just in time, they succeed at stopping the Machine from activating, successfully removing the Element of Magic. Twilight dons it, happy to finally have the Element. Unfortunately, as a result they greatly anger Queen Unity, who decides to try and kill them. Twilight manages to prevent a brutal attack and mind control attempt via the Tear of Chaos, but in the process, the Element of Magic is destroyed. Princess Cadence appears and distracts her mother long enough for Twilight, Pinkie, and Spike to escape, but they must continue to flee, for they are pursued to the Gate, which is locked away. Their victory was Pyrric: the damage has been done. Without the Element of Magic, their efforts have become fruitless.

END PART THREE

PART FOUR: IN WHICH TWILIGHT MUST CONFRONT HER OWN INNER FEARS AND DEMONS AND RESCUE THE ELEMENT OF MAGIC

Twilight, devestated and heart-broken over her perceived failure, goes into a depressive spiral. She feels she's rendered all their efforts meaningless. Though the CMCs mention it is possible to recover the Element of Magic, to do so would require access to their special laboratory, which is locked away in the Age of Atlantium. In order to gain access, they must first find a way past the lock on the Gate. This requires them to create a special time machine, integrated into a flying machine for the sake of simplicity. While some head to the Dead Future to work on the time travel device, Twilight stays behind at the DBT. Much time is spent on her analyzing herself and on everypony else doing the best they can to help her recover, and make it clear to her that they WON'T give up on her, nor will they give up on saving all of ponykind. Eventually, the CMCs succeed in creating the time travel device, and Twilight reluctantly joins the rest in heading back to the Age of Atlantium.

In the Age of Atlantium, they find and recover the time travel device the CMCs worked on to allow them to rescue the Element of Magic. They succeed in implementing it and reobtain the Element of Magic safely.


PART FIVE: IN WHICH TWILIGHT AND FRIENDS MUST FIX THE REMANING ISSUES IN TIME AND PROCEED TO THEIR FINAL BATTLE

The Elements of Harmony have been gathered, but they are still not yet ready. Chaos is still too strong. Starswirl the Bearded has been examining the Shard of Mystery and has come to a realization that will allow them to enhance the powers of the Elements of Harmony, but it will take time, and require acts that live up to the virtue they inspire, because the method of enhancement will tie the Elements more strongly to their wielders. Each pony of the Mane Six must go to a different time period and perform an act for their virtue, to both fix the remaining issues in time and to power up their Element. Spike feels a little left out, but the CMCs tell Spike they think they can whip up something to give him a boost too, and they will also work on a device that will enable Twilight and her friends to escape Chaos' pocket dimension once it is defeated, so they can survive.

In the Prehistoric Era, Fluttershy must perform a special act of Kindness, to ensure that the Dragonkin can live in peace with the Prehistoric Ponies.

In the Age of Atlantium, Twilight must perform a special act of Magic, to ensure that the survivors from Mare Atlantium can live new lives on the surface.

In the Paleopony Period, Pinkie Pie must perform a special act of Laughter, to bring joy to as many ponies as possible, an act that will compel the ponies, in time, to form Equestria.

In the Disharmonic Era, Rainbow Dash must perform a special act of Loyalty, to ensure that Celestia and Luna will be able to reign peacefully, and to prevent Luna's transformation into Nightmare Moon from causing her death.

In the Present, Rarity must perform a special act of Generosity, to give as much as she can to the people of the newly reborn Equestria, to ensure they continue to have peace and tranquility, even in the face of the threat posed by the City of the Damned.

In the Future, Applejack must perform a special act of Honesty, informing the Dead Future Survivors of everything that has occurred and that, if she and her friends are successful, they will cease to exist, because the Future will not be a destroyed wasteland.

With their tasks completed, and Spike given a strong boost in his combat abilities, as well as everypony newly created weapons and armor by the CMCs, and the special device needed to keep them from dying in the Pocket Dimension, Twilight and her friends gather together and say goodbye to the CMCs and Starswirl the Bearded, for they are not likely to return. With their goodbyes said, they board the Wings of Time and return to the Age of Atlantium, to attempt to board the City of the Damned.

The City of the Damned has numerous defenses, and while they do their best to avoid damage, they eventually crash land near its base, the Wings of Time ruined beyond repair, though everypony and Spike aren't hurt. With no way to turn back, they move on into the City, heading for the top, where Queen Unity awaits.

They fight many monsters along the way, powerful foes, even a spawn of Chaos much harder to defeat than the one that attacked in the Dead Future, but they struggle on, surviving, staying alive, eventually, finally, reaching Queen Unity. A madmare in any sense of the word, Queen Unity gives them no quarter, and they give her just as little, engaging in a massive battle to the death, where our heroes are the victor. Queen Unity's soul was bonded to the City, and with her dead, the City begins to collapse, falling into the ocean. Twilight performs a wonderous act of magic, slowing the City's descent enough to prevent it from creating a fatal tsunami that would have wiped out any settlements within one hundred miles of the shore. As the City plunges, the Mane Six and Spike are swept into the Pocket Dimension by Chaos Itself.

Chaos first attempts to conquer their minds as he did before, but with the Elements of Harmony, it is impossible. Our heroes use the Elements of Harmony to seal Chaos and themselves within the Pocket Dimension, protect their minds, and to weaken Chaos. The Elements also enhance their individual combat abilities. Chaos attempts to employ psychological tactics, but It fails. They easily defeat Its shell, and break inside to the interior.

Inside, they confront Chaos in Its true form, a massive Alicorn-like being with Dragon wings, a Manticore's tail, and eyes like a demon. It is accompanied by two Earth Ponies, two Pegasi, and two Unicorns, subunits part of Chaos Itself. Chaos, like the rest of Its species, has modeled Itself after the dominant life on the world of Equestria. The Mane Six and Spike attempt to argue with Chaos, but Chaos will give them no argument--It does not see them as anything but a threat to be eliminated. The battle is long, hard fought, as the landscape they fight in constantly switches between the various time periods, giving Chaos access to many different powers, especially for its subunits. Eventually, they wipe out the subunits one by one, even as Chaos continues to resurrect the subunits. Twilight eventually realizes that Chaos is attempting to wear them down so It can wipe them out, and they try a different tactic to stop Chaos from resurrecting Its subunits. It succeeds and Chaos is left to only Its Alicorn form. The battle continues to rage as they fight harder and harder, but finally, inevitably, the Harmony of their friendship wins out, and Chaos falls. The Pocket Dimension begins to collapse around them, and they use the device to escape, though it is left a mystery at the end of the chapter whether they escaped or not.

END PART FIVE

EPILOGUE: DREAMS ON THE SHORE OF ANOTHER WORLD

They find themselves in the End of Time, alive, successful. Their lives have been forever altered by their experiences. Starswirl the Bearded, happy to see the success of their adventures, tells them they must not dawdle, but should return to the Present, for the Gates have already started to fade, as has he. With his final act, Starswirl the Bearded ensures the CMCs and our successful heroes can return to the Present.

They find the Present different from how it has been throughout their entire journey. Without the City of the Damned, the Present has returned to a form similar to the one it had been when they first began their journey so long ago: a peaceful, happy Equestria, that has not seen war for over a thousand years, that will live on, under the watchful, caring eyes of its two Princesses. Twilight and her friends return to Ponyville, where they prepare to live a new life, happy and free. While nopony is the same as they were when they started, and while they may have to make new lives for themselves, the mark they made on history, the differences they have made in the lives of so many ponies, both past, present, and future, will live on forever. The story ends by telling what everypony will do with their new lives, and that Twilight and Pinkie Pie will be wed in a special ceremony. They are now, finally, at peace.

THE END