Logan comes back into Team X, which was founded by Nathaniel Essex to supposedly protect mutants from Bolivar Trask and his Sentinels. Trask is openly trying to eradicate mutantkind, but Essex turns out to be just as bad. He has been lying about being a mutant, stole mutant powers by grafting his wife’s X-gene into himself, and eventually decides that mutants themselves are not good enough, so he plans to use the Helix Engine to activate millions of dormant mutants and splice their abilities into himself. Along the way, Trask’s Reavers attack the Essex Institute and Leech dies, Deathstrike tries to use the Helix Engine in Japan and is killed when Logan shoves her into it, and Walter Langkowski is corrupted into Sasquatch by the Engine and eventually begs Logan to kill him, which Logan does. Trask is later captured by Team X and Logan kills him by stabbing him through the chest.
The biggest personal twist is that Logan’s memories are fake. Thirty years earlier he lived peacefully with a woman called Red. Essex tried to recruit Logan, telepathically triggered his berserker rage, and Logan killed Red with his own claws. Essex then repeatedly forced Logan to relive that moment until his mind broke, allowing him to rewrite Logan’s memories. Red is then revealed to have been a previous incarnation of Jean Grey. Jean is the Phoenix and is continuously reborn, so after Red died, Jean Grey was born with no memory of that previous life. During the present-day story, Helix energy restores Jean’s past-life memories, so she realizes she loved Logan before as Red.
Essex eventually takes control of Helix Sentinels and unleashes them. His mass activation plan partly succeeds, causing the mutant population to explode from around ten thousand to millions almost overnight, with enormous civilian casualties and mutants becoming publicly known worldwide. Logan, Jean, and Shiro fight Essex and a giant Helix Sentinel in Tokyo. Logan finally kills Essex, but the Helix energy awakens something buried inside him: Apocalypse’s influence and Logan’s identity as the Horseman of Death. Jean uses her Phoenix power to burn that influence out of him, but doing so wipes Logan’s memories again. Jean ends the game remembering their lives together, while Logan remembers none of it. He leaves Lowtown to figure out who he really is and why Apocalypse seems to know him, even telling Jean that he will see her again despite not truly understanding their shared past.
The sequel hook is Apocalypse. Sabretooth appears to die, but his post-story bio says he crawls out of a watery grave after hearing a voice from the Helix Engine identify itself as En Sabah Nur. He then goes looking for an ancient tomb and considers joining the Horsemen of Apocalypse. There are also explicit Apocalypse lines calling Logan his Horseman of Death and saying that Death’s turn is over and War is next. So the ending is basically: Trask and Essex are dead, Jean becomes fully aware of being Phoenix, Logan survives but loses his memories and leaves her, mutants are now publicly exposed across the world, Sabretooth survives, and Apocalypse is being set up as the next major threat.
