Warning: This article contains spoilers for the Ms. Marvel finale.
Ms. Marvel revealed that Kamala Khan is a mutant, changing her comic book origins connected to the Inhumans. This change likely aligns her with the X-Men when they appear in live-action, and they've been the subjects of major twists in Marvel Comics themselves. The biggest twists in Marvel history involve the mutants, including the recent shocking reveal concerning Moira MacTaggert.
Other all-time comic book twists likely play out in the MCU shortly as the Thunderbolts and Namor both emerge. All twists shock but not all succeed, and some Marvel Comics twists induced more head-scratching than jaw-dropping. Still, they potentially hint at future live-action developments as the MCU digs deeper in Marvel's rich comic book lore.
Namor Is A Mutant
Comic book fans know Namor predates the Marvel Universe, first appearing in Marvel Comics #1 in 1939. He formally joined the new Marvel continuity in Fantastic Four #5, with his origin as a half-human/half-Atlantean largely intact. His origins change in X-Men #6 from 1964 when Professor X suspects that Namor is in fact a mutant.
This ranks among Marvel's earliest and most significant twists given Namor's prominence in comic book history, and likely carries over into the MCU when he appears in Black Panther: Wakanda Forever.
Norman Osborn Is The Green Goblin
Another early shock for Marvel Comics readers involved the Green Goblin's true identity. Comic book fans today know the Green Goblin is Norman Osborn, but this remained a secret for many years. The Green Goblin first appeared in The Amazing Spider-Man #14 and the massive twist occurred two years later in The Amazing Spider-Man #38.
This upended everything fans knew about the early Marvel Universe and led to years more stories with rich conflict, culminating in Gwen Stacy's death at the Goblin's hands in The Amazing Spider-Man #121, among the most shocking deaths in Marvel Comics history.
Wolverine Has Bone Claws
Wolverine experiences several retcons from his first appearance in The Incredible Hulk #181, including the fact he was actually a mutant. Perhaps the biggest twist involving Wolverine occurred during the Fatal Attractions crossover event when Magneto rips all the adamantium from his body. Wolverine then pops his bone claws for the first time.
This twist added another layer of intrigue to Wolverine's mysterious backstory, suggesting the Weapon X program took advantage of the existing claws when giving him his iconic adamantium ones.
Jean Grey Didn't Die
Jean Grey dies in The Dark Phoenix Saga, easily among the best X-Men comic book storylines ever. A major twist in Fantastic Four #286 brought her back to life after several years. The issue, written and drawn by John Byrne, reveals the Phoenix Force placed the real Jean in a cocoon during the first encounter and the Jean who died was a cosmic facsimile.
Writer Kurt Busiek gets credit for Jean's return in the issue as he initially pitched the idea himself to Marvel Comics years before. This massive twist radically altered the X-Men's course in the 1980s, eventually leading to Jean's return to the team in 1991.
Iron Man Served Kang The Conqueror
Some twists left fans confused more than shocked. In The Crossing, a major if largely forgotten 1990s Avengers comic storyline, Iron Man kills Jarvis on his way to revealing he always served Kang The Conqueror. The twist undoes thirty years of continuity and ends with Iron Man dying and being replaced with a younger version from a different timeline.
The comics ultimately retconned the twist, mostly handwaving it away in the Heroes Reborn and Avengers Forever storylines that followed later in the 1990s and reestablishing the original Iron Man.
Xorn Is Magneto
The Jean Grey twist eventually paid off with new stories and possibilities in the comics, but another mutant twist didn't. New X-Men #146 reveals that the mutant Xorn had actually been Magneto all along. Magneto died years earlier in the comics, and the connection to Xorn generated more questions than it did answers.
Though Grant Morrison planted many clues in earlier issues the twist didn't last long. 2004's Excalibur #1 revealed Xorn wasn't Magneto at all, and Magneto was still alive on Genosha.
Spider-Woman Is A Skrull
A major comic book twist the MCU likely adopts in some form concerns Spider-Woman. Secret Invasion reveals that Jessica Drew, the original Spider-Woman, had been a Skrull imposter for years. Queen Veranke takes over Drew's identity and impersonates her as she orchestrates the all-out invasion of Earth by the Skrull Empire.
Rights issues complicate Drew's live-action potential, with Sony owning the Spider-Woman name, but Marvel Studios retains rights to Drew herself. Given her importance to the Secret Invasion storyline, she likely appears in some way in the upcoming streaming series.
Moira MacTaggert Is A Mutant
Writer Jonathan Hickman pulled off one of the biggest twists in Marvel Comics history in 2019 when he revealed Moira MacTaggert had been a mutant all along. The longtime X-Men ally revealed in House of X #2 she has died several times and retains memories of her previous lives, leading her to engineer the best possible future for mutants in this timeline.
This twist completely recalibrated Moira's entire comic book history, going back to her first appearance in The Uncanny X-Men #96. Her character continues to evolve as recent comics revealed her intentions aren't entirely pure.
Bucky Barnes Is The Winter Soldier
Comic book fans know Bucky Barnes died in battle, leaving Captain America in grief for decades. Bucky's death remained among the few comic book deaths untouched by retcons, at least until the early 2000s. Writer Ed Brubaker delivered a massive twist when he revealed Bucky survived and had become the Winter Soldier.
The Winter Soldier twist resulted in enormous narrative benefits for Captain America and the Marvel Universe and factors heavily in the MCU, where Bucky remains a key player in live-action.
The Thunderbolts
The Thunderbolts likely form in the MCU in the near future, given recent narrative developments in the franchise. If they do, the cinematic team likely plays off perhaps the greatest twist in Marvel Comics history. The Thunderbolts, a superhero team, revealed themselves to be the Masters of Evil in disguise at the end of their first issue in the 1990s.
Baron Zemo constructed the Thunderbolts to take advantage of the Avengers' apparent destruction, a development the MCU may adapt with the live-action Avengers in disarray at the moment.