1000 years in the future:
Colossus, Ernst, No-Girl, Anole and Glob Herman suddenly find themselves in a dusty landscape. Anole throws up, then apologizes. Colossus remarks he also found that very disorienting.
They find a door in front of them. Ernst tells them Martha wants them to turn around now. They find a huge pyramid with a stairways leading to a statue of Apocalypse. Ernst tells them No-Girl is picking up bad thoughts. They aren’t supposed to be here. Lord Apocalypse gave mutants their chance, but they are gone from this world now.
Where are they? Glob wonders. When are they? Anole replies. Apocalypse’s whole thing was ‘survival of the fittest’. Did mutants lose?
Colossus asks whose thoughts No-Girl is picking up. Ernst points upwards, where stand the Horsemen of Apocalypse, Venom, Deadpool and Man-Thing. Venom hisses that mutants aren’t allowed. Only the worthy survive! As they attack, Colossus shouts at the kids to take the Ark and take it to that doorway.
As they run, Ernst translates Martha’s thoughts that there is one Horseman missing. As if on cue, they are attacked from the ground by said missing Horseman - Moon Knight.
Colossus hits him hard and orders the kids to flee through that doorway. The other X-Men will come for him.
They run through the doorway and see what looks like several closed biotopes of different worlds in bubbles, linked to each other through pathways. Where are they? Glob asks sensibly.
They make their way through a dark, gloomy landscape. Glob is nervous. Anole points out they need to keep moving till they get to the next of these messed up bubble worlds. They need to find a place to hide until Colossus finds them.
They are stopped by a cute, little, goblin-like creature called Moogum. They tell him what happened and he explains their friend in Apocalypse’s world is lost to them. He suggests they keep going. But they don’t know where to go or where they are, Glob Herman protests. Moogum informs them this is Magika, domain of the Scarlet Queen and all that is mystical. There are many things that go bump in the night, with big teeth that would love to eat three mutants and a brain in a jar, but he will help them… for a price. He is hungry. If he helps them find the way, will they help him find dinner?
They agree and he instructs them on all the ways not to go, and finally the one that leads to Atlantis and then Computo world. They agree to go there and thank him. They offer him some food they got. Moogum grins and explains that, when he talked about things with big teeth, he meant Moogum. He turns into a giant monster and attacks, smashing Martha’s jar. Glob fires plasma at him, while Ernst scoops up Martha and they run.
They are on a raft, crossing a large body of water, arguing about whether this was a good idea. The idea is still to find safety and away to contact the X-Men. Glob Herman laments what will happen if they are stuck here. He will die a virgin. Anole addresses Glob’s crush on Jean Grey. He shows sympathy. He bets he will never get a chance to ask out Striker now.
Ernst is worried. Martha is getting quieter in her damaged jar. She can barely hear her now. Anole promises they’ll find her help in the next world.
On a high-tech world, they are discovered by a being in an Iron Man style suit, who asks why they have come to Stark-self. They ask about Tony Stark and are told his flesh died long ago but his creations live on. They are the last AI. More Starks join them and the first repeats its question. The youngsters tell their story. The Stark reply that mutants are forbidden on Omega World by Apocalypse. They have to leave or be destroyed. Apocalypse rules all – they cannot help them.
When Apocalypse rose again in the early 21st century the trials began. Entire races and civilizations wiped out. Apocalypse’s end game. The Atlanteans, the Inhumans, the Stark-Self, the Wakandans, the Mystics and the Moloids. These are the fittest. Those who remain. They cannot help them. Mutantkind has come and gone. Natural selection has decided their fate.
Glob Herman asks why Apocalypse hasn’t come after them and the Ark then, to which Anole suggests maybe he is giving them another chance. Waiting to see if they can survive on their own.
The Stark-self point out Apocalypse isn’t known for his benevolence but his ways are a mystery. Whatever reason, they must leave Stark-Self. But her friend is sick! Ernst announces helplessly, pointing to Martha and he shattered vessel.
Herman tries to tell her Martha is gone. She hasn’t heard her speak in weeks. The Stark-Self sense there is still an electrical impulse of the mind. Ernst asks them for help. The Stark communicate silently then announce the Stark father was an ally to the X-Men and would have helped them. So will they. Then they must leave.
The exhausted kids march through an arctic style steppe. The only one not exhausted is No-Girl, who now has a new mechanical body.
As they fend off a dragon, Glob remarks that circling back to Magika was a terrible idea.
A spider-world. Good thing he can regenerate, Glob tells Anole, who had to burn to get the new superstrong body he has now.
On the run, the kids realize Inhumans still don’t like mutants.
Walking through ruins, Glob wonder what Jean Grey is doing right now. Writing about him in her diary, Anole suggests. Really? he asks hopefully. No, Anole shoots back.
Fighting Mole Men.
Finally, they have reached the last world. It’s empty. No more mutants and they don’t know what to do.
Jean announces to the X-Men they’ve been here for a year. This Omega World is all that’s left. Logan tells her to get her head in the game, as the X-Men attack the Horsemen.
Storm orders the X-Men to protect the Ark. Colossus grabs her throat and announces she is too late. Everything they have been fighting for is over. Mutants’ time is over. So says Lord Apocalypse!