Well, here is how I would have re-written the later half of the show. Welcome to my world:

The whole season 6 invasion with the Changelings never happens at all. Chrysalis and the changelings had managed to re-group following their defeat in limited numbers. They would slowly rebuild over the course of season 6 and wouldn't be seen in it at all. Season 6 wouldn't have a villain defeat finale, instead it would have been some sort of Rainbow Roadtrip esque episode where they explore some ancient lost legend that mentions Grogar and the prophecy of the "Broken Heart" that mentioned something along the lines of "During the first conclude, the Heart of One trusted will turn as black as midnight". They are spooked by this, but think nothing of it. After all, it is just a legend, right?

Season 7 begins with the debut of Collapse in the show canon. She has a few episodes and shows off her wacky inventions with Twilight and her friends and becomes a re-occurring background character. Instead of the Storm King being in the movie, he is featured throughout the season. Magnolia is his right hand enforcer in place of Tempest Shadow. Tempest would still be there but would have a more minor role. What ends up happening is that the Storm King's invasion is the focus of season 7 with several episodes being a part of it.

Magnolia and Twilight have some extremely deep moments throughout their conflict, intense emotional scenes and duels. The Storm King preyed upon her vengeful side and basically was responsible for turning her into what she is now. Little did he knew, she was fully aware of this and let it happen. There is some sort of final battle in which the Storm King is defeated by Magnolia after Twilight and the others convince her of the magic of friendship, but Collapse would have been the one to truly change her heart. She strikes the Storm King down and he turns to Stone. The rest of his army are defeated or fled.

Season 8 focuses all on Magnolia's reform. Starlight would be there to help her in the reform process but unlike Starlight, Magnolia will remain a cold, utilitarian and calculating unicorn. She hasn't changed that much, just 'switched sides' if you will. Over time that slowly softens up but she still largely remains the same. The school of friendship, student 6 never happen. There is a lot of focus on the Dragons, Griffons, and even the Centaurs. Mainly an adventure based season with elements of slice of life, focus on background characters and other development. Zecora is also featured prominently in season 8. Mage Meadowbrook would still exist independently of the Pillars, as well as Somnambula. The Pillars never existed. The better episodes of season 8 would still exist, the ones you know and love but just without the school of friendship.

Season 9 would begin with the similar scene with Grogar you saw. He would free Sombra, Tirek, and the Storm King from their respective banishments or imprisonment. Chrysalis isn't present in this, as she was never defeated. She hasn't been season since season 3.

Grogar would look like this instead of some old guy. Instead of the Grogar you see in the show, he is intelligent, calculating, with some witty humor and of course the intense darkness, and evil within his heart make him a potent and unique villain. He is much like a force of nature.

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Grogar also caught the attention of two other characters. Magloria, you know her, and some witch character of sorts. The witch would be named Hercelius, and would also be an alicorn. She knows the secrets of the world through and through, her cutie mark would be some sort of key going into a keyhole. Magloria, Hercelius, The Storm King, King Sombra, and Tirek form our Legion of Darkness. Throughout season 9 they plan and plot. Of course in season 9 there are your usual episodes, the shining ones from the show with the added presence of Collapse and Magnolia, more focus on Starlight, Maud and Trixie.

Grogar would send his pawns to the depths of the world to retrieve the elements of disharmony or any equivalent artifacts. Those artifacts are recovered and are as follows. They are artifacts of the ancient gods that once ruled Equestria, and were used by the gods to overthrow the Titans that ruled long before that.

Magloria - Winter's Heart (Element of Gloom)

Winter's Heart is most often associated with the dying and the dead, as well as silence, cold, and the season of winter itself. It can be used to summon the dead, fill enemies with dread and despair, as well as bring about destruction. It has one final activation matrix, and when activated it will allow the user to achieve unlimited power. However that comes with a steep price, a date of death is set and it is unavoidable.

Lord Tirek - The Forge of Days (Wrath)

The uses and powers of the Forge are best represented through its most obvious symbol, fire. Fire is powerful, dangerous, and destructive, yet it also can be used as a tool in the right hands, to create and reshape. Also has association with nobility, wealth, and other expressions of power. The Forge of Days takes the form of a massive sledge hammer and is incredibly heavy to carry. Wielding the Forge of days, Tirek will become incredibly enraged and have insane destructive potential but his mental ability will be nearly non-existent as a drawback.

Hercelius - Word's Delight (Element of Deceit)

The Word's Delight isn't an artifact. It is rather an anomalous flame that the 'chosen' can step within and it will consume them and surge their power and alter their form to include purple flaming eyes. It entirely revolves around the openings of things: the opening of doors, the opening of the body, the opening of the mind. This allows Hercelius to have the power over keys, dreams, and the words she uses. Around her, you are more likely to believe what she says. However at any random point while the artifact is being used, it will randomly make the truth known.

Storm King - Harp of the Heart (Greed)

The harp is most commonly represented through music (particularly drums) and dance, expressions of vitality and motion. Storms, thunder, and the sea are also common symbols, as the contend to stir and quell these forces. The harp is commonly used to heal and invigorate the body and can also ward against a variety of perils both natural and supernatural. The Harp is an easy to use artifact, however at Maximum power it will cut 1/4th of your lifespan off.

King Sombra - Helm of Hubris (Pride)

The crown is commonly associated with conflict and strife, as well as all that entails and surrounds violence such as war, murder or bloodlust. It can be used to summon various spirits - commonly of a more violent vein. This will allow Sombra to gain power with increased violence and destruction around him. This makes it easier to drain magic from his foes. It comes with a cost, once used to its full extent it will completely destroy the user's ability to do magic on their own. If the crown is lost, than that user will no longer have the ability to do magic. Pride will be the user's downfall, and that is unavoidable.

They all successfully retrieve the artifacts, however Grogar knows they will all fall in the battle one way or the other. They were never intended to remain at his side, rather they are pawns to cause damage to the world so Grogar can unleash his full force upon the world when they are all weakened. The process to uncover these artifacts takes years, and season 9 had jumped ahead around 5 years.

In the years that had passed, the CMC are grown up and there are various other changes in the Mane 6, Collapse, and Magnolia's mane styles. Starlight is now a well renowned mage who has trained well with Twilight and Magnolia. Magnolia is sort of like Mace Windu in that she uses the powers of Darkness and Dark magic for well intentioned reasons. Using the powers of dark while remaining within the light.

The final plan of Grogar would begin with him sending King Sombra to conquer the Crystal Empire first. King Sombra easily defeats the leaders of the Empire using his Helm and refined power. He forces Cadence to betray Shining Armor and marry him in the process of corrupting her. This is the prophecy mentioned in season 6. Because this is the first invasion, he is the first to secure his reign over the Empire and like before he puts everyone into chains and forces them to fight for him like he did before. He bides his time and prepares, while the next phase begins.

Tirek goes to Canterlot. Thankfully most of the ponies there had evacuated because he was spotted on the way there with his massive sledge. With the Forge of Days, he lays waste to most and destroys a large part of the mountain that causes a massive collapse on the other side of it. Thankfully this doesn't destroy the entire city. With his enraged state of mind, he engages in battle with the 2 sisters and our heroes. Due to his inability to think for himself, the Forge is ripped from his hands and he is defeated. Tirek is banished into the Moon while the Forge of Days is to be guarded by the strongest and most powerful guard. It will basically be seen as a most honorable act to be among those who guard the artifact from those like Tirek.

Meanwhile in Ponyville, a snow storm has started. Magloria had begun her role and fills the entire population with dread and grief and takes over the town and surrounding landscapes. Magloria is able to destroy the Map Table and the throne room of the mane 6. Magloria is suddenly attacked by the heroes, the sudden attack causes her to almost activate the matrix but they reveal to her the true nature of the artifact. Upon that revelation, she gives up the artifact. There is some sort of scene in which she reveals who she really is, a zebra / pony hybrid and all that, she is forced to join the heroes in the future battles to avoid imprisonment in the future for what she did.

Now, the heroes are well organized as well as most of the ponies. The Storm King Invades, but this time they are all ready for him and his army is taken by surprise. He uses the Harp and does a mass amount of damage upon the landscape. The armies clash, and there is a stalemate. He uses the Harp at maximum power and what ends up happening is that he just dies instantly. The Storm King for whatever reason wouldn't have lived for much longer. The Harp is taken by the heroes and is put under protection along with the Winter Heart, guarded in a similar manner to the Forge of Days.

Hercelius is sent by Grogar to divide the heroes and the mane 6. She is successful for a time but due to the nature of the artifact the truth is revealed and she is easily defeated. Like with Magloria, Hercelius is then forced to join the heroes in the battles in order to earn her freedom by the end of the war.

The remnants of the Storm King's army are taken over by Grogar. Grogar releases his monsters upon the world and frees those who are in Tartarus. Given the desperation of our heroes, they are all forced to seek Chrysalis's aid. The Changelings by this point have completely modernized and their Hive is massive and resembles a massive city, and is completely modernized. A brief confrontation ensues, but they convince Chrysalis to aid them in exchange for Twilight to synthesize artificial love that replenishes itself for them to feed upon so they no longer have to starve.

The changelings join the Alliance (the name of the heroes in this war and their allies), while Grogar's army is known as the Legion. There are very intense battles across the land such as the battle of Las Pegasus in which Rainbow Dash and Lightning Dust worked together to drive out avian like monsters from invading. The war has forged close connections and common bonds. Magloria and Hercelius even became friends with Collapse, among others.

The Legion is extremely powerful and the Alliance's victories are especially hard-fought. The war itself will in total last about a year but what the ponies had gone through in total will make it feel much longer.

Grogar demands Sombra to join the Legion as he has been biding his time. Sombra refuses, and cuts a non-aggression pact with the Alliance that allows him to remain neutral. They cede him the entire frozen North. Cadence by this point is corrupted and is his loving life. Shining Armor had escaped and will never forgive them for the non-aggression pact, however accepts it as he sees the larger picture.

How Grogar is defeated, he is defeated by the combined might of the changelings, dragons, ponies, kirins, griffons, and the heroes. The elements of harmony banish him into the stars and the remnants of his army are put back into tartarus.

The war was insanely destructive to the land, and a new technology is invented by using the power of harmonic energy to heal scars, injuries and mental trauma. There is a massive conference upon the ruined grounds of Canterlot of which the Dragons, Changelings, Griffons, and others will officially unite with the ponies in a large Alliance that stretches across most of the known world for all times.

Celestia and Luna basically give up their rulership over Equestria. Starlight and Twilight are made the new rulers, Magloria and Hercelius are pardoned and given honors for their cause in the war, while a council is established between the leaderships of all the nations in the Alliance.

The damage to the land is repaired and the show ends with the various leaders in the future recounting the war a few years later, and then there is a party celebrating the 5 year anniversary of Global Unity and the victory in the war.