Marvel’s upcoming Secret Invasion show will delve deeper into the Skrulls’ perspective in the Marvel Cinematic Universe, which may include showing Captain Marvel in a more villainous light. Carol Danvers' past as a Kree soldier fighting the Skrulls is likely to have far more consequences than the Captain Marvel movie was able to address. Although Carol finally saw the Kree as the aggressors who were attacking Skrull refugees, her turnaround to help the Skrulls may not have been enough to redeem her in the eyes of some factions. Secret Invasion is set to change the MCU in big ways, and this more complex view of the MCU would have a difficult time avoiding making Captain Marvel into a villain.
Secret Invasion adapts a comic storyline in which the Skrulls planned an invasion of Earth following the destruction of their homeworld. They used their shapeshifting abilities to replace key humans, including superheroes, and some of these replacements were not even aware of their Skrull nature until they were activated by a code phrase. The show’s focus will be on this rogue faction of invading Skrulls, and Nick Fury and the Skrull Talos are set to return, but there are still few details about how Secret Invasion will handle the story.
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The MCU made a lot of changes from the Skrulls’ comic backstory that will affect Secret Invasion, such as making the Kree responsible for the destruction of their homeworld instead of the planet-eater Galactus. The motivation for the invasion in the comics was a prophecy that supposedly predicted the coming of Galactus, but that has to change for the show because Galactus isn’t involved. Instead, these rogue Skrulls may rally behind their mutual hatred for Captain Marvel and her allies. Given their tendency to replace superheroes in the comics, it would make sense that the Skrulls are working against the Avengers. Since any number of MCU characters could be Skrulls, it would be easy for the Skrulls to target the heroes they feel have wronged them.
Captain Marvel was an active participant in the Kree Starforce when they were at war with the Skrulls, and some Skrulls could hold her responsible for everything the Kree did while she was working with them - up to and including war crimes. Although Carol was also a victim of Kree manipulation, there’s no guarantee all the Skrulls would see it that way. When Captain Marvel returned to Earth and become one of its greatest heroes, that may have radicalized Skrulls against Earth, as well. Most of Captain Marvel’s backstory during the Kree-Skrull War is unknown, so the Skrulls may have more good reasons to harbor a grudge against her that Secret Invasion will reveal.
Secret Invasion has a chance to deal with the moral complexities of Captain Marvel’s backstory. Although Carol Danvers was kept in the dark and exploited by the Kree, she still took part in an extremely brutal war that cost the Skrulls their planet and sent them scattering as refugees. Since the time she first allied with Talos, Captain Marvel has tried to make up for the mistakes of her past, but that may not be enough when the Skrulls were left in such a desperate situation. Captain Marvel may be fighting the Skrulls’ real villains now, but in Secret Invasion, she would certainly be no hero to the rogue Skrulls.