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What is the plot?
What is the ending?
X-Men saves the Earth, but the victory tears the team apart in time. Jean and Cyclops are thrown far into the future with their son Nathan, while Xavier, Magneto, Beast, Rogue, and Nightcrawler are sent to ancient Egypt; Wolverine survives, though badly weakened, and Gambit is dead.
The ending begins with Bastion's plan collapsing as the X-Men fight to stop his Prime Sentinels and the larger extinction-level crisis he has triggered. Jean, empowered by the Phoenix Force, reaches Bastion and strips away the control he has over the transformed humans, breaking his hold on the attack. At the same time, the rest of the team is struggling to keep Magneto's Asteroid M from crashing into Earth, because Bastion's move has forced the entire planet into a final, desperate crisis. The situation becomes even more dangerous when the government launches missiles at the asteroid, making the threat worse instead of better.
Inside the conflict, Professor X pushes into Magneto's mind and breaks through to restore him. Magneto returns to full power and acts decisively, using that power to stop the asteroid from destroying Earth. The result is a final, violent release of the entire conflict: the X-Men are pulled away with the asteroid and scattered through time. The immediate battle ends, but the team is no longer together.
After the dust settles, the story jumps ahead six months. Forge is left behind at the ruined mansion, searching for the missing X-Men and finding no clear sign of them. Bishop arrives and tells him the team is not dead, but displaced through time. That explanation is then shown to be true.
Rogue, Nightcrawler, Beast, Magneto, and Xavier wake up in ancient Egypt in 3000 B.C., stunned to find themselves in a barren, unfamiliar world. There they encounter a young man known as En Sabah Nur, the being who will become Apocalypse. The scene makes clear that the group has been dropped into a dangerous time and place they do not understand.
In the far future, Jean and Cyclops wake in 3960 A.D. and find themselves with their son Nathan, who is still a child there and is being cared for by Mother Askani. Their ending is quieter but no less disorienting: they are separated from the rest of the team and forced into a future where their child exists before them in another form of time.
Wolverine's fate is left in a damaged but surviving state. He was still alive after Magneto ripped out his adamantium, but he is weak and removed from the main action by the end. Gambit's fate is the most final of all the major characters in the ending: he dies earlier in the season and does not return by the finale. Mr. Sinister survives the battle after Jean strips him of the mutant DNA he had stolen, leaving him ruined but alive. Bastion's fate is presented as likely death after the attack on Asteroid M, though the ending leaves that less certain than the others.
The final movement of the story is not just about survival, but about separation. The team wins the immediate war, saves the Earth, and prevents global destruction, but the cost is that the X-Men are no longer in the same time, the same place, or even the same moment of history.
Who dies?
Yes. In X-Men '97, several characters die, and the biggest cluster of deaths happens during the Genosha massacre in "Remember It" (episode 5), with additional confirmed deaths and a few off-screen confirmations later.
Gambit dies in episode 5 while trying to save Rogue and the other mutants during the Sentinel assault on Genosha. He attacks the giant Sentinel to stop it from slaughtering more people, is impaled in the process, and his final sacrifice leaves him mortally wounded; Rogue finds him afterward, confirming he is dead.
Banshee dies in the same Genosha attack when a Sentinel blasts him out of the sky and incinerates him. He is seen flying away to warn Rogue and others to seek shelter, but is then destroyed in a sudden, brutal burst of energy.
Marrow dies during the Genosha massacre as well, caught in the same Sentinel blast that kills Banshee. She is burned up in the attack while trying to escape the destruction.
Sebastian Shaw is confirmed dead after the Genosha assault. He is shown covered in blood and later treated as a casualty after the Sentinel attack wipes out large numbers of mutants and council members; later reporting and episode analysis identify him as one of the confirmed dead from the massacre.
Moira MacTaggert dies in the Genosha attack. She is shown amid the chaos as explosions tear through the area, and later coverage identifies her as one of the casualties confirmed after the massacre.
Callisto dies during the attack on Genosha as a result of the Sentinel onslaught and the wider destruction around the Morlocks. Later confirmation makes clear she perished after the chaos around Magneto and the Wild Sentinel.
Madelyne Pryor dies in the Genosha massacre. She is one of the major confirmed losses from the Sentinel attack, and later recaps describe her as having been vaporized or otherwise killed during the destruction of Genosha.
Magneto appears to die in episode 5 after the battle with the giant Sentinel. He sacrifices himself while trying to shield others, then is blasted in the final clash; the episode presents him as dead, though the show later leaves his long-term status part of the story's fallout rather than a simple clean finality.
Dazzler is counted among the Genosha dead in later coverage. Her fate is not always shown as directly as Gambit's or Banshee's, but post-episode confirmation places her among the casualties of the Sentinel attack.
Squid Boy is another Genosha casualty. He is shown among the badly wounded or unconscious survivors after the massacre, and later reporting confirms he died in the attack.
Leech and other Morlocks are also killed during the Genosha massacre. Coverage describes the Morlock community as being roasted or wiped out in the Sentinel assault, with Leech specifically included among those caught in the destruction.
If you want, I can also give you a clean episode-by-episode death list for X-Men '97 only, with separate sections for confirmed deaths and "appears dead / later confirmed dead."