X-Men '97 picks up several months after the events of X-Men and sees the X-Men questioning their future after an increase of sympathy towards mutants after the attempt on Xavier's life, with Cyclops and Storm wanting to continue on Xavier's dream and others such as Jean Grey wanting to create new lives for themselves, while Magneto is moved by the growing mutant sympathy and wants to follow in Xavier's footsteps as the team's leader.

Cyclops races to find the source of new anti-mutant technology.

When Magneto is forced by the UN to stand trial, a group of anti-mutant rioters test his resolve.

The team is propelled into a tragic confrontation with an immortal mad scientist.

Jubilee must relive the X-Men's greatest adventures when she's transported into a 16-bit video game.

Team members hit Genosha as UN honorees while a press event risks exposing the team's dirty laundry.

Storm is forced to face her worst fears in order to free herself.

The X-Men finds Sentinel inventor Bolivar Trask, realizing they've been played by a mastermind.

The X-Men must unite to face a new threat.

The X-Men work to settle the score before it is too late.

The X-Men's dream is put to the test as mutant-human relations reach a tipping point.