In 1995, on the Kree Empire's capital planet of Hala, Starforce member Verssuffers from amnesia and recurring nightmares involving an older woman. Yon-Rogg, her mentor and commander, trains her to control her abilities while the Supreme Intelligence, the artificial intelligence that rules the Kree, urges her to keep her emotions in check.
During a mission to rescue an undercover operative infiltrating a group of Skrulls, alien shapeshifters with whom the Kree are at war, Skrull commander Talos captures Vers, subjects her to a memory probe, and heads to Earth. Vers escapes and crashlands in Los Angeles. Her presence attracts S.H.I.E.L.D. agents Nick Fury and Phil Coulson, whose investigation is interrupted by a Skrull attack. In the ensuing chase, Vers recovers a crystal containing her extracted memories while Fury kills a Skrull impersonating Coulson. Talos, disguised as S.H.I.E.L.D. director Keller, orders Fury to work with Vers and keep tabs on her.
Using her extracted memories, Vers and Fury go to the Project Pegasusinstallation at a U.S. Air Force base, where they discover Vers was a pilot presumed to have died in 1989 while testing an experimental jet engine designed by Dr. Wendy Lawson, whom Vers recognizes as the woman from her nightmares. A S.H.I.E.L.D. team led by Talos disguised as Keller tries to capture them, but they escape in a cargo jet with Lawson's stowaway cat Goose. They fly to Louisiana to meet former pilot Maria Rambeau, the last person to see Vers and Lawson alive.
Rambeau and her daughter Monica tell Vers, who was once close to them, that her real name is Carol Danvers. Talos arrives and reveals the Skrulls are refugees searching for a new home and Lawson was Mar-Vell, a renegade Kree scientist helping them. Talos plays a recovered recording from Lawson's jet, prompting Danvers to remember the crash: Lawson attempted to destroy the engine's energy-core to keep it from the Kree, but was killed by Yon-Rogg before she could. Destroying the engine herself, Danvers absorbed the energy from the ensuing explosion, giving her powers but losing her memory.
Danvers, Talos, Fury, and Rambeau locate Lawson's cloaked laboratory orbiting Earth, where Lawson hid several Skrulls, including Talos's family, and the Tesseract, the power source of the energy-core. There, Danvers is captured by Starforce and interfaces with the Supreme Intelligence. During their conversation, Danvers removes the Kree implant that was suppressing her powers, allowing her to reach her full potential. In the subsequent battle, Fury retrieves Goose, who is revealed to be an alien Flerken. Goose swallows the Tesseract before blinding Fury's left eye. Danvers destroys a Kree bomber, forcing Kree officer Ronan the Accuser and his squadron to retreat, before overpowering Yon-Rogg on Earth and sending him back to Hala with a warning to the Supreme Intelligence.
Danvers departs to help the Skrulls find a new homeworld, leaving Fury a modified pager to contact her in an emergency. Meanwhile, Fury drafts an initiative to locate heroes like Danvers, naming it after her Air Force call sign, "Avenger".
In a mid-credits scene, set in the present day, the pager, which Fury activated prior to his disintegration,[N 1] is being monitored by Steve Rogers, Natasha Romanoff, Bruce Banner, and James Rhodes when Danvers appears and demands to know Fury's whereabouts.[N 2] In a post-credits scene set in 1995, Goose climbs onto Fury's desk and regurgitates the Tesseract.