A class of alien students is gathered around a holo-statue of Cyclops. The teacher, E’tha, tells them the story of Cyclops saving Earth when he sacrificed his life to stop Apocalypse. She goes on to briefly recap the history of the X-Men over the last 100 years. After Apocalypse’s defeat, Professor X led the Skrull mutants in search of freedom. These Skrulls decided to pursue justice across the universe. Over time, these new X-Men brought law and mercy to many worlds. Amongst many great things, they were able to stop Galactus by developing a self-replicating energy supplement for him. Afterwards, they established a central base for the Universal X-Alliance on the planet known as X-World in which they all currently reside.
As E’tha finishes her speech she finds all of her students are now looking out a nearby window. They’ve spotted one of the X-Men’s ships coming into port. Phoenix walks in and surprises E’tha. She hasn’t seen Jean in years and she still looks the same. After some small talk the focus switches to the kids. They are excited to see Iceman and General Fiz are there to greet the crewmembers of the newly arrived ship.
Down below, Professor X, Colossus and a newly evolved Storm exit the ship. Fiz greets Professor X whom he refers to as Founder-X. The Professor is happy to be back, but is tired. He requests some time alone. We see the students above are all psyched. Jean suggests that E’tha cancels class for the rest of the day. The students won’t be able to concentrate. E’tha agrees and the students run out of the room. As E’tha leaves she asks Jean if she’ll join her for the festivities. Jean tells her she’ll catch up.
She stays behind to look at Cyclop’s statue. She thinks to herself how hard it has been. She tells the statue of how she’s been a surrogate mother to many children over the years. She goes on to say that she never remarried. She starts to think about the love they shared and tears form in her eyes. She’ll always love him.
In the courtyard below, many people are gathered. An obese Beast and a spiky Iceman talk about the last few years. Beast has been off on a five-year mission with the Fantastic Four. Iceman is now an X-Alliance division leader. Storm interrupts and asks if anyone knows where Jean is. Iceman tells her she’s probably in the holo-museum. Nearby, Colossus introduces his two great-grandchildren, Anya and Marti to Marrow and Gambit. They look a lot like their deceased great-grandmother Kitty Pryde. It turns out that Gambit and Marrow got married. Their grandson is going to have triplets any day. Rogue joins the group, however she looks just as young as she did 100 years ago. Rogue lets them know she’s gained full control over her powers. At this revelation, Marrow pulls Gambit closer to her.
Elsewhere, Sunfire walks up to Cable and asks him how he’s doing. Cable tells him that he’s not really Cable, but Nate Grey. Last Nate’s heard Cable let the techno-virus take more control of his body. He thinks he’s even working for Magneto. Speak of the devil; Magneto walks in with Polarity (Lorna Dane), Cable and three other Brotherhood members. We find out one of their names is Tooth. Alliance-X members come over and are ready to fight Magneto and his crew. He tells them he’s here in peace. He wants to pay his respects to Xavier. After a short-lived debate Mags tells Charles why he’s there. He heard his health was deteriorating. Charles tells him that what he’s heard is true. He’s dying.
In the holo-museum Ororo tells Jean the same thing. Professor X may only have a few days left to live. Jean wants to know why he didn’t tell her. Storm tells her that he’s always felt responsible for Cyclop’s death. Which is the very thing that drove him and Jean apart. Charles loved Scott like a son and has always felt horrible about the whole thing. Storm wants Jean to forgive the Professor before he passes away. Jean tells her that it’s herself, not the Professor that she’ll never forgive.
Back with the Prof, he explains to everyone that he was exposed to a virus that has taken over his entire body. There is no way to stop it. Fiz butts in and tells him that a research team has found a device that could cure anything. A scientist continues the story. The machine is something that was created thousands of years ago. Unfortunately they can’t activate it. They’ve determined that it was designed to run off of primal bio-kinetics. They haven’t found anybody powerful enough to run it.
Professor argues that he doesn’t want anyone to risk his or her lives to save him. They all say they’re doing it anyway. Professor starts to argue, but falls over in his hover chair. Nate rushes over and examines Charles. Beast asks the scientist who was explaining the machine to them if he knows how to operate it. He instructs them to place Xavier within the receptacle and then to position themselves at specific power terminals. The final step is to charge the machine up with their powers. It starts working and the scientist tells them he needs more power. Charles yells out to them. He wants them to stop. He tells them it’s a trick. It’s too late however. The scientist transforms into his true form, Cyclopalypse. After the original circuit was destroyed, he created another conduit and they just provided the power he needed.
After his first two attempts didn’t work, he created a reality in which he was supposedly defeated. Now he has the power he needs. The Living Monolith is still with him and channeling their powers. Xavier tells him that he won’t win. They won’t actively use their powers to charge the circuit anymore. Cyclopalypse tells him that he’ll reverse time 100 years and with the conduit in full operation he can drain the powers of 100 years of their lives. He’ll start over from that point in a world without X-Men. Xavier tells him that it can’t happen.
Cyclopalypse reverses time and the X-Men and company revert to their original forms. Professor attempts a mind link, but Jean denies him. She wants to try and contact Scott. She enters Cyclopalypse’s mind and finds Scott inside. He’s fighting from within. Somehow, he’s channeling their energies back to them. Suddenly, the circuit explodes. They find themselves back in Egypt. Cyclopalypse blames the Monolith for being too weak to channel the energies. Cable jumps up and heads over to the now fallen Cyclopalypse. Jean uses her telekinesis to stop him mid-air. At Cyclopalypse’s command Monolith teleports them both away.
An enraged Cable yells at Jean for stopping him. He has waited all this time to stop Apocalypse from destroying the future. Jean tells him that Scott is still inside. Cable tries to convince her that Scott is dead. Jean tells him she sensed him through their special rapport. She looks to Xavier for support, but he still hasn’t sensed him. Jean starts to cry and Storm comforts her, telling her it’s all over.
(Two days later)
At the Xavier Institute, Professor is outside thinking to himself. He thinks he’s failed his students, especially Scott and Jean. He doesn’t want Cyclops’ sacrifice to be in vain. On the brighter side, he’s happy that Wolverine is recovered from being Death, Horseman of Apocalypse. He wonders what will happen with Magneto and Polaris now that they left together. He also wonders what will happen with the mutant Skrulls. He looks away and sees a taxicab approaching.
The taxi is for Jean. As she gets inside, Professor wonders if what Apocalypse showed was true. Will they grow further and further apart in the future? The ghost of Cyclops will always be between them. Jean drives away leaving Xavier behind.