A year ago at San Diego Comic Con, Marvel Studios announced that Academy Award winner Brie Larson has been chosen to play Carol Danvers, also known as Inhumans. Recently the Skrulls became an even greater threat to Earth's heroes in the 2008 crossover event Secret Invasion - and this is where the Skrulls arriving in the Captain Marvel film could alter the very fabric of the MCU.Created by writer Brian Michael Bendis and Leinil Francis Yu, Secret Invasion was essentially the Marvel Universe's version of Invasion of the Body Snatchers. It revealed that after the Kree/Skrull War, a coalition of Earth's superheroes who dubbed themselves the Illuminati - Iron Man, Doctor Strange, Mr. Fantastic, Namor the Sub-Mariner, Black Bolt of the Inhumans, and Professor Charles Xavier of the X-Men - invaded the Skrull homeworld to warn them against further attacks on the Earth. The heroes were subsequently captured and experimented upon before escaping.Armed with knowledge of Earth's superhumans from their experiments, the Skrulls, who believe the Earth is "religiously and rightfully theirs," mounted a secret invasion of the Earth. They captured and replaced several superheroes, as well as infiltrating S.H.I.E.L.D. The Marvel Universe was destabilized and thrown asunder by suspicion and mistrust - the event's slogan was "Who Do You Trust?" - as anyone could have been revealed as a Skrull. The end result saw S.H.I.E.L.D. disbanded by the President of the United States and replaced with an organization called H.A.M.M.E.R. led by Norman Osborn (the Green Goblin). Osborn formed his own secret evil version of the Illuminati, which included Doctor Doom, Emma Frost, and Loki, leading into the Dark Reign storyline.
By setting Captain Marvel in the 1990s, Marvel Studios looks to be laying out a long game involving the Skrulls that could ultimately lead to a Secret Invasion of the MCU. We won't know until the film is released how Carol Danvers gains the powers of Captain Marvel, but Marvel Studios President Kevin Feige has announced younger version of the famed super spy has two working eyes - therefore Captain Marvel could depict the events that caused Fury to lose the use of his left eye.
There are also bigger questions Captain Marvel must answer: if she was active since the '90s, where has she been and why hasn't she been mentioned by anyone before? One answer could be that Captain Marvel's adventures are cosmic in nature and her exploits took place in deep space. The concept art seems to that, showing Danvers in battle with Skrulls in what looks like a Skrull space craft. In addition, if she was d with the S.H.I.E.L.D. of that era - which could mean welcome cameos by Agent Peggy Carter (Hayley Atwell), Howard Stark (John Slattery), Hank Pym (Michael Douglas), Avengers: Infinity War, which will allow her to take her place among the superheroes of the present day MCU.
The long-term ramifications of the Skrulls in the MCU is what's most exciting - and terrifying - about a potential Secret Invasion. The Skulls could have been on Earth for decades, even before Carol Danvers became Captain Marvel. It's possible they never left. The Skrulls could have been in the MCU this whole time - which could mean some characters we've been watching for years could secretly have been Skrulls all along! The Skrulls have the ability not just to look like humans but to mimic superhuman powers and abilities, so potentially be anyone could be a Skrull - from Clint Barton (Jeremy Renner) to Scott Lang (Ant-Man) to even Tony Stark himself!
The MCU has already faced massive destabilization when it was revealed in Captain America: The Winter Soldier that Hydra had existed within S.H.I.E.L.D. since the agency's inception in the 1950s. After the Civil War over the g of the Sokovia Accords resulted in the Avengers breaking apart and the imminent arrival of Thanos armed with the Infinity Gauntlet, a Secret Invasion by the Skrulls would be a game-changer that would wreak an untold amount of havoc on the already precarious state of the MCU.
Phase 3 of the MCU will culminate in Avengers: Infinity War, with the sequel to MCU would need its young superheroes more than ever, as the heroes and fans alike will ask each other Who Do You Trust?