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- I. Subzero's Birth
- I-I. Crystals
- Articuno, Rayquaza, and Kyogre are introduced
- Groudon's death is explained
- Sceptile and Charizard are introduced
- Kyogre is killed by Sceptile
- Sceptile and Charizard kidnap Articuno
- Britt, Howard, and Dessum are introduced
- Howard and Dessum begin a battle
- Rayquaza is attacked by Regice for territory reasons and crashes in Iceponte City
- Howard and Dessum's battle is interrupted by Rayquaza
- The group of teens and Rayquaza head off to find Articuno
- Feraligatr is introduced as Sceptile and Charizard's leader
- Rayquaza and the others face off against Sceptile and Charizard
- Britt's Snorunt evolves into Froslass and defeats Sceptile
- Rhydon is introduced
- Rhydon and Charizard continue their assault
- Rhydon is overwhelmed and creates a massive earthquake
- The Frozen Plateau collapses and Rhydon falls into the ocean, presumed dead
- Charizard is defeated and reveals that they are now in possession of the Freeze Crystal, a powerful artifact with unknown potiental
- Articuno is freed
- The group learns that Sceptile and Charizard are now targetting the Flame Crystal, located in the Cavern of Silence, guarded by the Regi Clan
- Regice is banished from the Regi Clan
- Sceptile and Charizard kill Regirock and mortally wound Registeel and Regigigas
- Wielding the power of the Flame Crystal and Shadow Crystal, Charizard transforms
- Charizard attacks Iceponte City
- The teens and their allies are defeated by Charizard
- Tom is introduced and saves them from death, and defeats Charizard with his Alakazam, although Articuno was captured again
- Regice collapses in the middle of frozen nowhere and dies
- The group gathering the Crystals for evil purposes is revealed as Elemental Shadows
- Elemental Shadows HQ is rumored to be in Dauten, a city not far from Iceponte City
- The teens begin their journey to Dauten, now crossing the Adira Desert
- Ivan is introduced as one of two humans in Elemental Shadows
- Feraligatr is revealed as Ivan's partner
- With the Freeze and Volt Crystal, Feraligatr transforms
- I-II. Erebos
- Regigigas attacks Feraligatr
- Ivan and Feraligatr retreat to Elemental Shadows HQ, now revealed to be in the Adira Desert
- Sceptile and Charizard appear
- Charizard kills Tom
- Sceptile dies trying to protect the teens from Charizard's attack
- The group enters the HQ and is greeted by the leader of E.S.
- Andrew, the leader of Elemental Shadows, is introduced as a black haired boy with dreams of conquering the planet
- Charizard attacks Andrew, only to be killed in one hit
- The group defeats some of Andrew's Pokemon
- Britt and Froslass battle Andrew's Electivire
- Britt is saved by Howard's Salamence
- Articuno is once again freed
- Andrew unleashes his most powerful Pokemon, Garchomp
- Dessum is left alone to battle Andrew's Heatran and Metagross
- Andrew places Garchomp back into his ball and sets it on his desk, along with the four Crystals
- An impenetrable barrier surrounds Andrew and light from the Crystals blinds everyone
- Andrew combines with the Crystals and Garchomp, and the HQ is destroyed in the process
- The new being names himself Erebos and the Crystals fall from his body and smash
- The Crystals begin to react to Britt and Articuno, and merge into a single white Crystal, the Light Crystal
- Using the Light Crystal's power, Britt and Articuno combine and create Amaterasu
- Amaterasu revives everyone she has seen die
- Erebos and Amaterasu each launch a powerful wave at each other
- Everyone but Ivan, Feraligatr and Rhydon, who are now silent after hearing Erebos treat them like nothing, join the beamstruggle and begin to attack Erebos
- Rhydon's anger builds and he evolves into Rhyperior
- Rhyperior attacks Erebos and Amaterasu's attack overwhelms them both
- Rhyperior is killed and Erebos defuses
- Andrew is presumed dead, but not Garchomp
- Entrusting Feraligatr, Sceptile, and Charizard to Dessum, Ivan attacks Garchomp as he threatens to self destruct and bring about the death of everyone there
- Garchomp explodes and Ivan is killed, but the others are saved
- Everyone now intends to fight as a group for the benefit of others
- The group's name is made Subzero, in memory of the final attack Amaterasu launched, Subzero Burst
- The wreckage of Elemental Shadows HQ is rebuilt as Subzero HQ
- II. Subzero, the Protectors of Yorita
- II-I. The Adventures of Subzero
- Froslad is introduced as Dessum's old friend
- Dessum and Froslad recall how they got their first Pokemon, Riolu and Mawile respectively
- The mystery of Dessum's cracked Ultra Ball is explained in the tale, caused by the Riolu breaking out
- Andrew's past is explained as an abused boy who vowed to seek revenge on everyone that caused him pain
- Andrew returns, revealing he was not dead, and that he fused with a Mewtwo a shard of the Light Crystal, which became a Shadow Crystal shard upon his touch
- The fusion of Andrew and Mewtwo is introduced as Chaos, and launches an assault on Iceponte City
- Chaos is brought to justice and is completely obliterated when Articuno and Britt fuse back into Amaterasu
- Aleister is introduced
- Dessum battles a teenager in the Adira Desert, who reveals himself as Aleister, and specializes in sandstorm Pokemon
- Aleister joins Subzero
- Aleister and Dessum assist Cresselia in a fierce battle and defeat Darkrai
- II-II. Erebos' Revenge
- Britt plans to meet with her brother from Osla, John, and his friend, Neal
- Howard encounters a strange boy named Ray, who claims that Subzero HQ belongs to him
- Ray is revealed as Andrew's minion
- Ray reveals to Howard and Britt that Garchomp barely survived his explosion, but was saved by Ray
- Using a shard of the Shadow Crystal, and the ashes of Andrew and Ivan, Ray revives them both
- Andrew kills Ray and takes Garchomp
- Dessum greets John, Neal, and Froslad as they continue their journey to Subzero HQ
- The four boys are attacked by the newly reborn Erebos
- Dessum instructs Froslad to find Aleister and the other members
- Two of Erebos' 'admins' appear, Roy and Luis
- A battle between the admins and the three teens begins
- Erebos disappears
- As Dessum is knocked unconscious, he sees Ivan attacking Roy and Luis
- Froslad and Aleister encounter Erebos on the way to Subzero HQ
- Froslad chooses to battle Erebos on his own, and Aleister runs off towards the HQ once more
- Aleister arrives at Subzero HQ, and fills in Britt and Howard on what has happened
- Howard heads off to help Froslad, while Aleister and Britt head into Dauten to find Tom
- Britt and Aleister inform Tom, and his friend Josh, of the situation
- Josh joins Subzero
- Howard finds Froslad in an enormous crater, near death
- Before passing out, Froslad tells him that Erebos has gone back to Iceponte
- John and Neal are beaten
- Luis escapes
- Froslad is rushed into the hospital by Howard and his wounds are treated
- Josh, Tom, Aleister, and Britt arrive in Iceponte
- Howard joins the four others and they hurry to the battlefield
- Erebos returns to greet Dessum with a third admin, Vincent
- Erebos snaps his fingers, and dozens of people appear, revealed as minions of Erebos' army
- The five members of Subzero join the battle
- Luis returns
- John and Neal wake up
- Roy and Ivan begin fighting a block away from the fight between the army and most of Subzero
- Vincent instructs Luis to assist Roy, who is now battling Neal, John, and Ivan
- Dessum leaves the hospital with Froslad, now healed from his battle with Erebos, and head for the smaller fight taking place
- John is defeated again
- Neal pins Roy against a wall holding a dagger
- Dessum's Lucario, still at the scene, finishes off Roy's Gengar
- Roy and Neal fight for the dagger on the ground
- Erebos appears and tells Dessum and Froslad that all of Yorita is under attack
- Dessum and Froslad arrive at the scene
- Roy retreats
- Dessum is defeated by a soldier
- Luis defeats Ivan
- Luis and his Umbreon are beaten by Neal
- Erebos tells the Subzero members fighting his army what he told Dessum and Froslad, and disappears once again
- Froslad kills the soldier with the dagger
- Josh and Tom head to a radio station and send out a message, warning the people of the incoming armies
- Erebos tries to stop Tom from talking, but Josh intervenes and begins to fight him
- Froslad discovers that the soldiers are all robots
- Froslad's Xatu heals the fallen Ivan, John, Dessum, and their Pokemon
- Tom and Josh escape
- Erebos disappears yet again
- Tom and Josh return to battle
- Infernape explodes, and ends up killing itself, the soldiers around it, and Vincent
- Froslad, Dessum, Neal, John, and Ivan head to the giant fight taking place
- The soldiers are defeated everywhere
- II-III. Rematch
- Erebos appears, enraged
- Britt and Articuno use a shard of the Light Crystal and fuse into Amaterasu
- Erebos' power dramatically increases, and he transforms into who he calls Hellfire
- Howard and the others realize that they too can fuse with a Pokemon with a shard of the Crystal
- Howard and Rayquaza fuse into Apollo
- Neal and Gallade become Nemesis
- Ivan and Feraligatr become Poseidon
- Froslad and Milotic become Fontus
- John and Kingdra become Kratos
- Aleister and Tyranitar become Vulcan
- Josh and Flygon become Aeolus
- Dessum and Lucario become Helios
- Tom and Alakazam become Mars
- The last fight between the fusions and Hellfire begins
- After an hour of battling, only Helios, Amaterasu, Apollo, and Hellfire are left standing
- Helios is defeated
- Apollo distracts Hellfire as Amaterasu powers up a gigantic rainbow ball attack
- The attack is fired, but Hellfire managed to redirect it towards Apollo and Amaterasu
- The others regain consciousness and help push the sphere back towards Hellfire
- The sphere envelopes him, but Hellfire absorbs all of the power and transforms into Omega
- Omega now plans to not only conquer Earth, but the whole universe
- Roy and Luis awaken
- Helios and the others all fuse simultaneously with one final shard of the Crystal
- Roy and Luis quit Elemental Shadows and watch a brilliant white light in the sky, along with the rest of Iceponte's population
- The fusion is complete and successful, and names himself Hyperion
- Luis and Roy accept an offer to join Subzero as Hyperion spots them
- Hyperion and Omega begin battling
- Hyperion is defeated, and the people of Iceponte lose hope
- Erebos launches a red ball, with the intention of having it destroy Earth's core, ending the planet and everyone on it but him
- Subzero's Pokemon, and the people of Iceponte's, all fire a powerful attack on Erebos
- Erebos creates a giant black ball to oppose the multicolored wave of light
- Britt and Articuno grab a shard off the ground and fuse, then chase after the red ball fired earlier
- The Regi Clan arrives and joins the beamstruggle
- Amaterasu destroys the red ball
- Earth's inner core begins to crack apart as Amaterasu leaves
- Amaterasu returns and defuses
- Joining hands, all of Iceponte fuses in a flash of bright light
- The new fusion, Alpha, defeats Omega for good
- The planet begins to shake as the core cracks apart
- Ivan sacrifices himself and his spirit becomes Earth's new core
- The last shard is given to a young boy named Callum
- Everyone in Iceponte is made a member of Subzero
- Several years pass
- III. The Terror of Majin
- III-I. Dracoblaze Attacks
- Dessum is now a middle school teacher
- The boy who was given the shard, Callum, catches his very first Pokemon, Nosepass
- Andrew and Garchomp awaken in a purgatory and meet Anubis, god of eternal judgment
- Anubis reveals that time in the afterlife is much slower than the world of the living, and several years have passed in the living realm
- Anubis realizes that Andrew may have some good in him after all, and gives him one hour to think, during this time is when the years pass
- Andrew tricks Anubis into returning him to the realm of the living and is brought back from the dead, stronger than ever before
- Andrew pays a visit to Dessum's house and confronts him, with revenge in mind
- Strange red suited men charge inside and Dessum is shot in the shoulder
- Dessum passes out and awakens in a jail cell
- A guard nearby reveals that Andrew was also captured
- Andrew escapes his cell and defeats the guard
- Andrew defeats the guard at Dessum's cell and frees him
- Dessum chooses to follow Andrew
- After fighting several more guards, Andrew and Dessum are attacked by who appears to be the leader
- Dessum and Andrew escape the prison and find themselves east of Dauten
- Andrew reveals that the man they fought was Steven, the previous leader of Elemental Shadows
- Anubis begins to see the good in Andrew once again
- Andrew and Dessum are attacked by Steven once again
- Steven reveals that he used a shard of the Shadow Crystal to fuse with his Charizard, and is now known as Majin
- Majin also reveals that he is the new leader of Dracoblaze, an organization with three goals: kill Andrew, kill Subzero, and world conquest
- Andrew and Dessum manage to escape again
- Subzero holds a meeting at Dessum's house
- During the meeting, they are attacks by Dracoblaze's minions
- It is revealed that Tom, Neal, Froslad, Roy, Luis, and Aleister have all been captured
- Callum joins Subzero
- Andrew and Howard fight off the minions and they retreat
- Subzero plans to storm Dracoblaze HQ
- Andrew heads off during the night to fight them alone
- Neal breaks out and attacks the guards with Andrew
- Andrew begins fighting Majin
- Neal is defeated
- Andrew and Neal are captured yet again
- Dessum, Howard, John, Britt, and Callum begin their journey to Dracoblaze HQ
- The five members are attacked by more minions
- Callum's Nosepass evolves into Probopass during the battle
- Everyone but Howard and Rayquaza are captured
- Howard and Rayquaza use the shard to fuse into Apollo and rush to Dracoblaze HQ
- Apollo convinces the people of Dauten to assist him, and they launch an all out assault on Dracoblaze HQ
- Apollo defuses and Howard runs further into the building to free Subzero
- Subzero is freed and everyone combines into Hyperion
- Andrew battles Majin as Hyperion assists Dauten's people in the fight against Majin's army
- Majin's army is revealed to consist of robots, much like Andrew's was
- Majin kills Andrew
- Anubis reveals that Majin has taken over the world and that Iceponte, Dauten, and Subzero are hiding at an underground base in Dauten, planning an attack
- Anubis gives Andrew one last chance to prove he deserves to live, and returns him to the realm of the living
- III-II. The Fight Against Majin
- Andrew returns
- With the last Crystal shard, everyone in the base, including Andrew, fuses
- The new fusion, Phobeus, speeds off to challenge Majin
- Phobeus and Majin begin battling above Dauten
- Majin powers up to maximum and calls himself Perfect Majin
- During his transformation, Perfect Majin destroys all of Dauten
- Perfect Majin annihilates a small portion of the Eastern Forest
- Phobeus is defeated and defuses
- Andrew finds himself unable to combat Perfect Majin any longer
- Ivan appears for a split second and delivers a punch to Majin's face, then disappears
- Howard and John are killed
- In a fit of rage, Andrew transforms
- Andrew rips off Perfect Majin's arm
- Perfect Majin reveals that he has regenerative powers and regains his lost limb
- The purgatory begins to collapse after Anubis sends Howard and John back to the realm of the living
- Andrew and Perfect Majin launch a massive wave of energy at each other
- Anubis disappears forever along with the purgatory and Ivan
- Spurred on by Anubis' last words, Andrew's attack overwhelms Perfect Majin, and he is completely obliterated
- Now that Dauten is a giant crater, the people of Dauten and Iceponte work together and build a new city west of Iceponte, New Dauten
- Dauponte Bridge is built to connect the two cities
- Britt offers Andrew to join Subzero, but he refuses and disappears
- A girl named Luka informs another female of Steven's demise
- The second woman vows to get revenge for the death of her brother Majin
- Three years pass
- IV. An Assassin's Desires
- IV-I. The Sister From Hell
- Luka and Sarah, two underlings of Steven's sister, head towards Subzero HQ
- Andrew intercepts the two and begins battling them when Luka mentions Steven's sister is their leader
- Andrew reveals that her name is Malissa
- Dessum and Howard come outside the base and see the three fighting
- Sarah and Luka retreat
- Andrew is offered another chance to join by Howard and disappears
- Andrew and Howard follow Sarah and Luka
- Malissa's castle is revealed to be west of New Dauten
- Malissa plans to set thousands of robots upon Yorita, starting with New Dauten
- Malissa notices Andrew and Howard sneaking around and orders Sarah and Luka to pursue them
- Andrew and Howard escape from their and warn New Dauten of the incoming attack
- The army is defeated with ease
- The large Light Crystal shard is smashed into several smaller ones
- Callum and Probopass fuse for the first time and become Sisyphus
- Apollo, Amaterasu, Kratos, Sisyphus, Helios, and Andrew head for Malissa's castle
- Malissa reveals that she has hired a skilled assassin to deal with the intruders
- Apollo and Andrew chase after Sarah and Luka
- The assassin's name is revealed to be Cody
- Apollo chooses to battle Malissa on his own when she reveals another person is going to attack the others
- A Lugia appears and kills Sarah and Luka in a display of power
- Malissa's Shadow Lugia proves to be a formidable enemy
- Andrew chases after Cody
- Utilizing a shard of the Shadow Crystal, Cody combines with a Blaziken
- Andrew and the others confront the new fused assassin
- Helios and Kratos head to the scene of the other fight to assist Apollo
- The fusion of Cody and Blaziken addresses himself as Hades
- Helios saves Howard and Rayquaza from near death and carries them outside the castle
- Andrew begins fighting Hades
- Sisyphus leaves to help Kratos and Helios
- Helios shields Kratos from a devastating attack and falls to the ground in defeat, and defuses back into Dessum and Lucario
- Just as Hades begins to overpower Andrew, Andrew transforms
- Hades' power reaches maximum
- Andrew is defeated
- Amaterasu carries Andrew away from Hades as fast as she can
- Hades launches a blast of energy and everything in the castle is caught in the explosion
- One hour passes
- The castle is now a giant pit, and the members of Subzero are all unconscious
- Britt awakens to find that Lugia is dead
- Malissa also wakes up and pulls a dagger out of her pocket
- The dagger falls to the ground, and the two begin to fight
- It is revealed that Howard and Rayquaza escaped the blast, and show up on Tom's doorstep with a plea for help
- Tom and Josh fuse with their Pokemon and head to the ruins of Malissa's castle
- Aeolus and Mars arrive in time to see Britt kill Malissa
- One week passes, and everyone slowly recovers, except for Andrew, who is now dead
- IV-II. Cody's Assault
- The successor to Anubis is revealed as Thanatos
- Thanatos has no choice but to send Andrew into the depths of hell
- A mysterious dragon knocks Andrew out
- Garchomp confronts Andrew when he awakens
- Andrew and Garchomp begin fighting
- It is revealed that Druddigon was the dragon who attacked Andrew, not Garchomp
- Garchomp reveals that the new god of judgment is Zeus, not 'Thanatos'
- Andrew realizes Thanatos was Hades and attempts to find a way back, leaving Garchomp
- Most of the world's population is killed by Hades in a rampage
- Hades attacks Subzero
- Hades unleashes his Zoroark on the members of Subzero
- Druddigon and Andrew battle
- Druddigon is eliminated and Andrew discovers the portal to the purgatory, guarded by Hydreigon
- Hydreigon allows Andrew to pass through
- Dessum is killed by Zoroark, along with his Lucario
- After a Night Burst, only Britt, Howard, Aleister, and Tom still stood breathing
- The four remaining members of Subzero combine with their Pokemon
- Vulcan and Mars are killed
- Apollo and Amaterasu are chased by Hades, his mind set on killing them
- Andrew meets with Zeus and travels back to Earth
- Andrew transforms and flies as fast as possible to the scene in the sky
- Amaterasu is hit by a blast and defuses
- Articuno is killed seconds later
- Apollo defuses and Rayquaza is killed
- Andrew saves Britt and Howard
- Hades uses a second shard of the Shadow Crystal to merge with his Zoroark
- Andrew's strength increases to a whole new level
- Andrew and Reaper, the name of Cody's new form, begin fighting
- Zeus and the people of Earth had gathered in the purgatory and watched the battle through a large screen Zeus created, cheering Andrew on
- Reaper begins to overpower Andrew
- All of Earth, as well as Zeus, combine with a shard of the Light Crystal
- The godlike fusion, Soul, saves Andrew from an inevitable death
- Reaper unleashes his maximum power and names his final form Shadow Majin
- Shadow Majin annihilates Soul, and the people of Earth are thrown into a portal leading back to the purgatory
- Shadow Majin follows them, leaving Andrew beaten on the ground
- Garchomp escapes hell and returns to Earth after taking the Light Crystal shard from the purgatory
- Garchomp and Andrew fuse and follow Shadow Majin through the portal
- Shadow Majin arrives and launches a massive wave that will kill everyone and cause the people of Earth to disappear forever
- Earth retaliates and launches thousands of beams of their own, and the battle seems equal
- Zeus and Earth begin to lose the beamstruggle
- The fusion of Garchomp and Andrew arrives
- Apex, the new fusion of Garchomp and Andrew, destroys the wave heading for everyone else and instructs Zeus to send them all back to Earth through a portal
- Shadow Majin and Apex begin fighting in the air when the ground begins to crack apart
- Apex stops fighting and tells Shadow Majin there's no point in continuing, then defuses
- As Andrew and Garchomp head for the portal, Shadow Majin kills Garchomp
- Andrew's power reaches its pinnacle and he resumes fighting Shadow Majin, fueled by rage alone
- Shadow Majin loses several limbs and collapses on the ground, begging for mercy
- Andrew gives Shadow Majin enough of his own energy to survive the purgatory's eventual explosion
- Zeus reveals that when the purgatory is destroyed, he will also disappear forever
- Magma envelopes the portal
- Shadow Majin attacks Andrew and is killed
- Andrew searches for a way back to Earth as the purgatory collapses under him
- The purgatory explodes with Andrew still on it
- Zeus transports everyone to the place they were just before Hades' attacks
- Zeus disappears
- Fifty years pass
- V. Mokushiroku's Plot
- V-I. No Mercy
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