Following the shocking events of last week's episode, the X-Men '97 finale - "Tolerance Is Extinction - Part 3" - begins with a visit to the past and the moment Charles Xavier told his friend, Magnus, that he was a mutant.
We soon learn this is all in Magneto's head, with Professor X using his immense psychic abilities to force his friend-turned-foe to undo the damage he's inflicted upon the Earth. He succeeds, but Bastion is far from done and still has an army of Prime Sentinels on hand.
Just as the villain is about to kill Cable, Jean Grey returns as the Phoenix (briefly) to deal with him and leaves Mister Sinister a husk of his normal self. However, Bastion takes advantage of the distraction to take the Techno-Organic Virus from Nathan and transforms into his ultimate form.
On Asteroid M, Wolverine remains unconscious, leaving the remaining X-Men to fend off Bastion's attack (the team on Earth eventually shows up in a modified Sentinel).
It's a brutal battle which ends when Cyclops orders the team to stop fighting and offers Bastion their help. He refuses and when Earth's leaders unleash the "Magneto Protocols" missiles on the base, he seemingly allows himself to be destroyed rather than stand alongside the X-Men as a mutant.
While all this is happening, Charles manages to get through to Magnus and, just as it looks like the heroes will die stopping the asteroid from hitting Earth, the Master of Magnetism awakens and stops it...only for that and the mutants to suddenly vanish!
Six months later, the X-Men are still missing, presumed dead. A heartbroken Forge has tried and failed to assemble a new team and is suddenly met by Bishop who reveals that they're still alive...someone just sent them hurtling through time, and it's down to these two to find them.
In Egypt, 3000 B.C., Professor X, Magneto, Rogue, Nightcrawler, and Beast encounter a young En Sabah Nur. Meanwhile, in the future 3960 A.D., Scott Summers and Jean are confronted by Clan Askani and their son, a young Nathan Summers. Unfortunately, there's no mention of Wolverine, Storm, Jubilee, and Sunspot, and the episode ends with "To Be Continued..."
A mid-credits scene takes us to the present day and sees Apocalypse walk through the ruins of Genosha. He pulls a charred playing card from the rubble and says, "So much pain, my children. So much death," with the implication being that Gambit will be resurrected as Death, a member of his Four Horsemen of the Apocalypse!
That lines up with the comics and it's fair to say season 2 can't get here soon enough...