Without his dark side, Magneto became a blank slate character called Joseph (we don’t have time to get into all of that). But Xavier didn’t just destroy Magneto’s dark side. Instead, he took it inside of himself.
That dark side welled up inside of Xavier, subtly changing his behavior over a period of 18 months before eventually manifesting in the form of an unstoppable monster called Onslaught, a strange melding of Professor X and Magneto. Onslaught immediately became a problem bigger than the X-Men and, because this was Marvel in the ’90s, led to a company-wide crossover. By the end of the story, Onslaught had killed both the Avengers and the Fantastic Four.
Now, because of Franklin Richard’s ability to warp reality, the Avengers and Fantastic Four were rebooted in the absolutely horrific Heroes Reborn event (source of the heavily-memed drawing of Captain America with distended pecs). That led to another pseudo-reboot called Heroes Return, which was largely excellent.
As for the X-Men, Onslaught’s rampage caused mutants to become even more feared and hated. Which allowed Bastion to gain power and access to Professor X who, wracked with guilt by what Onslaught had done, turned himself in to the authorities.
This short summary doesn’t do justice to the mess that was the Onslaught storyline, of course. Magneto and Xavier have always been mirror images of one another, so there’s a logic to exploring their connections in a single character. But rather than examine the characters, Onslaught made their dark sides into a giant monster who smashes things. The editorial mandate that forced a reboot of the Avengers and the Fantastic Four only further muddies the waters, making Onslaught less an X-Men story about two of its most complex characters and into an indistinct mess.
Obviously, X-Men ’97 isn’t following quite the same trajectory. But “Bright Eyes” ends with Bastion holding Magneto hostage, delivering an unnerving monologue about mutant submission. And Bastion also notes that he’s keeping tabs on Xavier, who is very likely on his way back from Shi’ar space as we speak.
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