The Kree-Skrull War is a huge storyline within Marvel Comics universe, and now that conflict exists within the Marvel Cinematic Universe as well. Captain Marvel showed the Earth-born Carol Danvers joining this war originally fighting for the Kree empire, but then later aiding the shapeshifting Skrulls, as they were depicted much more sympathetically than they usually are on the printed page. Carol’s defection marked a major turning point in the MCU’s Kree-Skrull War, but according to Marvel Studios president Kevin Feige, it didn’t necessarily mark its conclusion. Speaking about introducing the Skrulls in Captain Marvel, Feige said:
Given the commercial success of Captain Marvel and the many positive reviews it’s received, it’s a good bet that Marvel will give the green light to Captain Marvel 2 eventually. While Kevin Feige’s above comment doesn’t confirm whether or not the Kree-Skrull War is still going in the present day, the conflict obviously played a huge role in Carol Danvers’ origins, and her actions might not have spelled the end of this bloodshed. We’ll have to wait on more official confirmation, but evidently Captain Marvel 2 will explore the Kree-Skrull War further, either directly or through the fallout.
Kevin Feige also elaborated on why it was decided to feature the Skrulls in Captain Marvel, saying the following in the Captain Marvel Official Movie Special (via Comicbook.com):
He’s absolutely right. The Skrulls were introduced in 1962’s Fantastic Four #2, and while various members of this species frequently fight Marvel’s First Family, the Skrulls as whole evolved into a threat against all the heroes of the Marvel Comics universe, particularly in the Secret Invasion storyline. That said, in sharp contrast to their usual depiction in the comics, Captain Marvel positioned the Skrulls, who were advertised as the movie’s main villains, as the victims in the Kree-Skrull War, with the Kree destroying their homeworld and intent on wiping out all of these shapeshifters.
Carol Danvers, who had spent years believing she was Kree and fighting for Starforce as Vers, eventually learned the truth from Talos and discovered how her mentor, Dr. Wendy Lawson, a.k.a. Mar-Vell, had defected from the Kree empire to help the Skrulls find a new home. After her powers fully awakened, Carol sent Yon-Rogg and the rest of the Kree operatives who had come to Earth packing, and she left to help the Skrulls find a new planet to live on. We have no idea yet if Captain Marvel 2 will be set in the 23-year gap between Captain Marvel and Avengers: Endgame, or if it will be set post-Endgame, but either way, this particular narrative isn’t over.