Arguably, one of the more surprising moments from season 1 of X-Men ’97 is the reveal that Jean Grey was held prisoner by Mr. Sinister and replaced with clone Madelyne Pryor.
It wasn’t so much that the writers were adapting an infamous plotline from the comics, it was how they did it. As a viewer, particularly if you watched the original 1990s cartoon, you were just as blindsided as the X-Men were. It’s unsettling to think that a character you’ve been following all this time is really a clone and you have NO IDEA when the original was swapped out. It’s an emotional arc that questions the concepts of family and identity.
When Did The Switch Occur?
For the longest time, nobody really knew when Jean was swapped out for Madelyne. It was a mystery until former X-Men ’97 showrunner Beau DeMayo confirmed on his X/Twitter account that the swap took place during “Beyond Good and Evil,” the four-part, season 4 finale of the 1992 classic X-Men: The Animated Series (X-Men ’97 is a continuation of the original series).
During “Beyond Good and Evil,” Apocalypse was kidnapping all the powerful psychics in the world so he could kill them all in one swoop inside the Axis of Time. The plan was to use the wave of energy that act would unleash to stop time and recreate existence where he rules unchallenged.
Master geneticist Mr. Sinister was working alongside Apocalypse, but he had his own agenda. When he found himself alone with Jean Grey in the Axis of Time, he made a clone of her to hand over to Apocalypse while he kept the real Jean to himself.
This means that the Jean we see in season 5 of X-Men: The Animated Series, the one who married Scott Summers (Cyclops) and was pregnant at the start of X-Men ’97, was a clone this whole time. Talk about a plot twist.
How Did the Truth Come Out?
At the end of the second episode of X-Men ’97 “Mutant Liberation Begins,” a woman appears at the X-Mansion door who looks just like Jean Grey. Only problem is the Jean everyone knows is inside the X-Mansion, having just given birth to her son Nathan Summers.
In the next episode “Fire Made Flesh,” Beast runs some tests that confirms the woman at the door is the real Jean Grey. The woman everyone thought was Jean is actually her clone. Jean and Madelyne share the same memories except for the ones involving Madelyne’s pregnancy and giving birth to Nathan. The only real difference between the two is that Jean’s genetic structure is older.
The X-Men aren’t sure what to make of the situation. Scott is devastated to learn that his wife and mother of his child is not the woman he loves. Madelyne is horrified and heartbroken to discover her entire existence is a lie.
Later in the episode, Beast discovers that Mr. Sinister is the one who created Madelyne, right as he materializes to manipulate the troubled woman. Obsessed with Scott and Jean’s genetics, he made Madelyne with the sole purpose of conceiving a child with Scott, one with unimaginable power.
Once Madelyne learns the truth, Sinister activates a device he’d implanted in her mind that accelerates her breakdown. She transforms into a much darker persona called the Goblin Queen and takes Nathan back to Sinister.
The real Jean saves the day by reaching out to her clone. She shows Madelyne the one memory they don’t share: her giving birth to Nathan. The moment and her love for her son breaks Sinister’s hold on her.
Unfortunately, during the chaos of trying to rescue baby Nathan, he’s injected with a deadly strain of a Techno-Organic virus that Beast can’t cure. Madelyne is the one to convince Scott to allow Bishop to take Nathan to the future in hopes of finding a cure, knowing they’ll probably never see their son again.
After Sinister is defeated and Nathan is sent to the future, Madelyne decides to leave the X-Men. She renames herself Madelyne Pryor and leaves to create a new life for herself.
How the Madelyne Arc Was Originally Told in the Comics
The comics version of this story is grimmer and more convoluted.
In the original 1980s Uncanny X-Men run, Jean was assumed dead following the events of the Dark Phoenix Saga. A grieving Cyclops met Madelyne Pryor as a cargo pilot in Alaska. He was rattled by Madelyne’s resemblance to Jean to the point he began to question if she was Jean reincarnated. Despite his suspicions, he fell in love with her. The two would eventually marry her, and have a son named Nathan.
Then Jean came back and everything went straight to hell (both figuratively and literally). Cyclops abandoned Madelyne and Nathan to reunite with his old girlfriend. Madelyne warned Scott that if he walked out the door, he shouldn’t come back. He left anyway and re-joined the original X-Men in a new team called X-Factor.
The cruelty of that rejection, on top of later discovering her entire existence was fabricated, drives the comics version of Madelyne into villainy. She’s manipulated by demons who offer her the revenge and power she feels she’s entitled to after everything that was taken from her.
What do we get from this offer? Inferno, an epic crossover event where Madelyne turns New York City into Hell itself. The event ends with her death. The fragment of Phoenix Force that had given her life abandoned her and returned to Jean, its preferred host.
X-Men ’97 compresses this story while making significant changes to it.
The biggest change is that Scott doesn’t abandon Madelyne when Jean returns. Him and Madelyne decide to separate in the animated series and he’s portrayed in a far more sympathetic light.
Also, Jean doesn’t inadvertently take everything from Madelyne. She reassures Madelyne that her experiences were real and that she deserves to exist as her own person. And while Madelyne does die halfway into season 1, it’s because she’s a victim of the Genosha massacre where she’s vaporized by a Sentinel.
X-Men ’97 Does Madelyne Justice
Madelyne Pryor is not a villain in X-Men ’97. She’s someone who thought she was building a life for herself, only to have it all dismantled in front of her. Her transformation into the Goblin Queen here is a combination of suffering from Sinister’s manipulations and being pushed to the brink.
While it’s sad she was killed off, the show did a good job of treating Madelyne with the same seriousness it gives to the main team’s story arcs. This is what separates X-Men ’97 from a typical superhero show. It takes something as surreal as a woman learning she’s a clone and turns it into an emotional gut punch that doesn’t shy away from the consequences a revelation like that brings.
Season 1 of X-Men ’97 is available to stream in its entirety on Disney+. Season 2 will premiere on July 1, 2026.
