The season one finale of X-Men '97 concluded with a post-credits scene that directly sets up the primary antagonists for season three, featuring the return of Apocalypse and the emergence of Mystique leading the Brotherhood of Mutants. This revelation follows a tumultuous season two finale where X-Factor leader Valerie Cooper, alongside Cable and his X-Force, attempted to prevent Apocalypse from possessing Gambit. Although Gambit was seemingly killed, Rogue managed to save him and, with the aid of a Celestial, imprisoned Apocalypse within a gem. Kurt Wagner sacrificed himself during this ordeal, ensuring Gambit and Rogue's safety.
The immediate aftermath of these events is fraught with peril, as the post-credits scene reveals the election of Graydon Creed as president. Creed, known for his staunch anti-mutant sentiments, is expected to revive the Sentinel program, presenting a significant new threat to mutants. The scene depicts Valerie Cooper in Washington, D.C., reviewing a redacted threat assessment file on Mystique. The situation quickly escalates when the real Cooper is killed by Mystique, who was disguised as her.
Mystique's file contains several notable Easter eggs, including references to her children: Graydon Creed, Kurt Wagner, and Rogue (Anne-Marie Darkholme). Her alias is listed as Raven, but the file also acknowledges previous actresses who portrayed her, such as Randall Carpenter, Jennifer Dale, Rebecca Romijn, and Jennifer Lawrence. The file also displays mugshots of her known associates, including Magneto, Blob, Toad, Quicksilver, and Scarlet Witch. Critically, the file states Mystique is determined to attack the United States, a resolve she seemingly confirms.
Despite Apocalypse having killed Magneto in season two, Mystique will now lead the Brotherhood of Mutants in season three, positioning them against both threats to mutantkind and the X-Men themselves. While Mystique, the Brotherhood, and President Graydon Creed are established as the season's main villains, the series has a history of introducing multiple antagonists. Season one included threats like Bastion, Mister Sinister, Adversary, and Mojo, while season two, dominated by Apocalypse, also featured the Brood, Exodus, and Danger. The extensive rogues' gallery available for X-Men '97 suggests a mix of episodic and overarching threats for the upcoming season.
Production for X-Men '97 season three has already been completed, with a planned release in 2027. While a specific date has not been announced, the premiere is anticipated for the summer. The series has also been renewed for a fourth season, implying that further narrative threads and villainous reveals will continue to unfold in subsequent installments.