Times after Captain America’s airplane crash, Howard continues to test the Tesseract to learn further about it. Ultimately, Project Pegasus is created byS.H.I.E.L.D to deal solely with studying the Tesseract. Over time, a Kree by the name of Mar-Vell ever infiltratesS.H.I.E.L.D under the name ofDr. Wendy Lawson. She becomes the head of Project Pegasus and relocates the Tesseract to her secret lab in space. She continues to work as part of Project Pegasus to produce a Light-Speed Machine. Though she's a Kree she doesn’t authorize her people to obliterate the Skrulls (a race of shape-shifters). She wants to hand the Skrulls the Light-Speed Machine so they can escape. She’s also intimately stowed down a bunch of Skrulls in her Space Lab. Before she can complete her work, a Kree squadron, led by Yon-Rogg, finds her in 1989.
Mar-Vell has asked a youthful airman, Carol Danvers, to accompany her and the two of them get shot down. This airplane has a Jet Engine that Mar-Vell has erected, and this is powered by the Tesseract (which is still safe in space). Yon-Rogg kills Mar-Vell. Carol shoots and blows up the spurt machine. Ever, she ends up absorbing all the energy from the explosion. Given the closest thing to the Light-Speed Machine has been blown up, Yon-Rogg takes Carol with him as she might be the key to figuring out the Engine. The Kree uses Carol’s amnesia to make her believe she's a Kree too. To keep her powers at bay, they put an asset on her. Six times pass.
In one of the operations in 1995, Carol is captured by the Skrulls who are trying to get to the position of the Secret Lab. Long story short, Carol ends up on Earth, runs into a youthful Nick Fury, finds the lab, remembers her Earth life, realizes the Skrulls are good, gets the Tesseract (which is inhaled by an alien cat), removes her asset, unleashes her full powers, takes down all of the Kree, and set the Skrulls free. The fantastic cat scrapes Nick Fury’s eye causing him to lose it, and he gets his notorious eye patch. Carol gives Nick Fury a pager-on-steroids which he's to use to call out to her only in case of a vital exigency.
Captain MarvelPost-Credits Scene
The alien cat spits up the Tesseract. This is howS.H.I.E.L.D reclaimed the Tesseract after it has been in Mar Vell’s secret lab. It technically noway leftS.H.I.E.L.D, it was always part of Project Pegasus.