X-Men '97 season 2 episode 4, Rise of Apocalypse: Part II, concludes with one of the series' most significant developments as Apocalypse kills Magneto during the final battle in Ancient Egypt. The episode depicts Magneto as dead after Apocalypse vaporizes him while he attempts to protect Professor X and stop En Sabah Nur. Episode 4 provides no indication that Magneto survived or that his fate differs from what is shown on screen.
Despite the X-Men's efforts to change history, they fail to prevent En Sabah Nur's transformation, leaving Apocalypse undefeated. Professor X ultimately returns to the present carrying the loss of his longtime friend, Magneto, and a renewed belief that Apocalypse cannot be stopped through compassion alone.
Meanwhile, a post-credits scene featuring Wolverine, Captain America, and Black Widow shifts the story back to the present and sets up the next phase of the X-Men's mission.
The ending of X-Men '97 season 2 episode 4 confirms Magneto’s death during the fight against Apocalypse. When Bishop arrives to rescue the trapped X-Men, Professor X and Magneto resolve to stay in Ancient Egypt for one more effort to stop En Sabah Nur from becoming Apocalypse. Magneto momentarily persuades Nur to accept an alternative, but the scheme falls apart when Nur finds they've traveled through time to change his fate.
The other X-Men escape through Bishop's time portal, but Professor X and Magneto stick behind to face Apocalypse. Even fighting together, they can't stop him. Apocalypse ultimately vaporizes Magneto in front of Professor X, showing no sign he survives. Magneto's last act is a sacrifice as he stays behind to safeguard his allies and the civilians targeted by Apocalypse.
A big theme in X-Men '97 season 2 episod e 4 is whether history can be reversed. The episode depicts that Professor X and Magneto’s attempts to change En Sabah Nur’s future actually help set the stage for the events that led to his transformation into Apocalypse.
Professor X tries to appeal to Nur with compassion and understanding, while Magneto feels that their common experience as mutants can convince him to turn away from violence. They join in urging him to choose a different way.
In the end, they don't make it.
Nur takes this as proof his fate is sealed when the X-Men arrive from the future to halt his ascension. His intervention does not alter his future, but it does affirm his notion that only the strong survive, and he accepts his identity as Apocalypse.
The conclusion also signifies a turning point for Professor X. Throughout the two-part story, he holds fast to the belief that every mutant has the ability to choose a different future. But after seeing the death of Magneto and the devastation of Apocalypse, Professor X realizes that he cannot change the fate of Apocalypse by persuasion alone.
By the end of the episode, Professor X has lost Magneto in the struggle and returns to the present. The consequence leaves him with no doubt that Apocalypse is a menace like no other and that its acts are impossible to stop by changing the past.
Although the episode revolves around the apparent death of Magneto, it jumps to the present day in a post-credits sequence. Captain America and Black Widow hand over Weapon X information to Wolverine, which suggests that there is something else about him to discover later on. After obtaining the information, Logan declares that it is time to reunite the X-Men.
In addition, the arrival of Captain America and Black Widow in the same episode also marks their first appearance in the X-Men '97 season 2. All things considered, this marks the end of the Ancient Egypt sub-plot of X-Men '97 season 2 episode 4 as the origin of Apocalypse and the efforts of the X-Men to change the course of history have been confirmed.