Back when Kevin Feige first announced that the Skrulls would be the villains in Captain Marvel at San Diego Comic Con, Marvel fans have had visions of Secret Invasion dancing in their heads. That comic book event from a few years ago had Skrulls replacing many heroes in the Marvel Universe, and was one of the more popular events following the first Civil War.
In an interview with Collider executive producer Jonathan Schwartz confirms that the Skrulls in Captain Marvel are planting seeds for future movies.
“Yes, we talked about Secret Invasion. I wouldn’t go into this movie saying, ‘Which one of these superheroes is a Skrull?’ Because Carol is more or less the first superhero to show up on Earth. But are we planting seeds for future movies? Always.”
There has been a rumor for a while that Skrulls will also appear in Avengers: Endgame. The rumor says that Clint (as Ronin) is hunting down Skrulls in Japan who are disguised as Yakuza. This is seen in the trailer:
It obviously wouldn’t be a big plot point in Avengers: Endgame, but it could be something to continue the seeds that Captain Marvel plants towards a larger Secret Invasion style storyline in Phase 4 of the MCU.