What If…? season 1 was often a gloomy affair, revealing various alternate realities that ended in death and destruction. The finale undid some of that, though, by bringing together the Guardians of the Multiverse to defeat Infinity Ultron and his quest for multiversal domination. A few of the dark timelines were fixed in the process – for instance, Killmonger being removed from his world and Dystopian Black Widow finding a new home.
After he was done sending the other Guardians back to their proper universes, the Watcher elected not to return Natasha Romanoff to Infinity Ultron’s world, where she was the last person left alive, and instead took her to a universe that had lost its own Black Widow – the setting of episode 3. Nat returned during this reality’s version of The Avengers and, with the element of surprise, was able to best Loki by snatching his scepter and putting him to sleep with it – similar to Captain America’s move against his younger self in Avengers: Endgame.
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While this was a much-needed happy ending for this Natasha variant, the scene actually creates a big Loki plot hole when you remember the specifics of episode 3. After Thor was killed by that reality’s Hank Pym, Loki led the forces of Asgard to Earth to get justice for his fallen brother, eventually simply deciding to take the planet for his own. In doing so, he skipped his exile from his homeworld which led to his alliance with Thanos in the Sacred Timeline. In other words, Loki really shouldn’t have his Mind Stone scepter here.
It’s understandable how this error happened in the first place – as ScreenRant points out, the writers and animators simply based this scene on The Avengers and so featured Loki’s iconic weapon from that movie. And maybe we can come up with a suitable explanation. It’s possible Thanos reached out to Loki once he started his assault on Earth and lent him the scepter to assist in his attack, under the provision that he hand him the Space Stone when he’s finished.
The complete first season of What If…? can be streamed on Disney Plus now.