In 1995, on the Kree Empire's capital planet of Hala, Starforce member Vers (an ex-U.S. Air Force fighter pilot and member of an elite Kree military unit called Starforce whose DNA was altered during an accident, imbuing her with superhuman strength, energy projection, and flight) suffered from amnesia and recurring nightmares about an elderly woman.
Yon-Rogg (Starforce's commander and Vers' mentor, who trains Vers to wield her new talents) trains her to control her abilities, which Yon-Rogg claims were bestowed upon her by the Kree. The Supreme intellect, the artificial intellect that rules the Kree, advises her to keep her emotions under control. According to the Supreme Intelligence, Vers is a victim of the Skrull expansion, and they have also invaded her home world. This led to the attack that gave Vers nightmares. The Supreme Intelligence persuades Vers that she has been given a gift by Kree and that she has to serve the Kree people. Vers was unaware that she had a device installed on her neck that suppressed her powers and allowed the Kree to control her.
Vers is tasked with rescuing an undercover officer who has infiltrated a group of Skrulls, alien shape-shifters with whom the Kree are at war. The assignment is on Torfa, a Kree border planet, and the operative has been working underground with Skrull for three years. However, the mission was an ambush prepared by the Skrulls. Vers is abducted by Skrull warlord Talos. Vers' memories are probed, which leads them to Earth. Talos sees in Vers' memories that she was an Air Force pilot on Earth who collaborated with Dr. Wendy Lawson to develop a new light-speed engine that can aid Skrulls win the fight against Krees.
Vers regains consciousness and faces Talos. Talos claims that these were her memories, which the Kree suppressed. Talos claims that the Skrull are seeking Dr Lawson and her light-speed engine and are on their way to Earth based on coordinates gleaned from Vers' recollections. Vers escapes aboard a Skrull escape pod, which crashes near Los Angeles. Vers communicates with Yon-Rogg and informs them that she is on planet C-53(Earth) and also mentions that Skrulls are looking for Dr. Lawson. She gets disconnected after Yon-Rogg mentions that they gonna reach Earth in the next 22 hours. Talos and the Skrull begin tracking Vers on Earth. Her presence draws S.H.I.E.L.D. agents Nick Fury(the future director of S.H.I.E.L.D., who is currently a low-level bureaucrat) and Phil Coulson(a rookie agent of S.H.I.E.L.D. who works closely with Fury), whose investigation is disrupted by a Skrull attack.
During the subsequent chase, Vers finds a Skrull crystal with her extracted memories, while Fury kills a Skrull impersonating Coulson. Talos, posing as Fury's S.H.I.E.L.D. commander Keller, tells Fury to collaborate with Vers to chase the Skrulls.
Vers and Fury travel to a US Air Force base to visit the Project Pegasus installation, which she has taken memories from. They discover Vers was a pilot who was presumed to have died in 1989 while testing an experimental jet engine designed by Dr. Wendy Lawson (Wendy appears to Vers as an artificial intelligence that is the collective embodiment of the Kree people's greatest minds and the ruler of the Kree Empire), whom Vers recognizes as the woman in her nightmares. Fury also takes up Goose, a cat from the Pegasus installation.
According to the institution's records, Wendy and a pilot died in the crash of the experimental engine, and the facility has been attempting to cover up this billion-dollar failure ever since. Only Vers knows that the pilot was herself. She also deduces that Lawson was Kree based on his penmanship. Concerned about the cover-up of these events, Fury asks S.H.I.E.L.D. for assistance, and Keller responds with force.
Fury instantly realizes that Keller is a Skrull (Keller calls by the name ‘Nicholas’ when everyone calls him Fury) and assists Vers in fighting his way past his fellow S.H.I.E.L.D. agents to escape in a plane with Lawson's stowaway cat Goose. They go to Louisiana to see former pilot Maria Rambeau, one of Vers’ oldest friends and a fellow Air Force pilot who goes by the call sign "Photon" and is the last person to see Vers and Lawson alive. Vers calls Yon-Rogg again, informing him that Lawson is developing technology to help them win the fight against the Skrulls. He denies that Vers ever visited Earth, claiming that the evidence she discovered consisted solely of Skrull simulations and mind games.
Rambeau and her daughter Monica inform Vers that her real name is Carol Danvers and that she was like family to them before they believed she had perished. Talos appears at Rambeau's house and informs her that the Skrulls are refugees looking for a new home, and Lawson is Mar-Vell, a renegade Kree scientist assisting them. Talos plays a recovered recording of Lawson's jet, prompting Danvers to recall the crash: When Lawson and Danvers were testing the speed-light engine, Kree started to attack. Because of that, they get crashed, and Danvers notices blue blood coming out of Lawson.
Lawson mentions that her real name is Mar-vell and she is from Hala planet. Lawson also asks Danver to save them (without mentioning whom) from the Kree’s war. Lawson attempted to destroy the engine to protect its power core from the Kree but was killed by Yon-Rogg before she could. Danvers destroyed the engine herself, absorbing the energy from the resulting explosion, granting her the energy core's powers but causing her to be captured by Yon-Rogg, who erased her memory.
Danvers, Talos, Fury, and Rambeau discover Lawson's covert laboratory orbiting the Earth. To protect Skrulls from Kree, Dr. Lawson has safeguarded them in her laboratory for all these years. It houses several Skrulls, including Talos' family, as well as the Tesseract, the energy source that powered Mar-Vell's engine. Starforce arrives and connects Danvers with the Supreme Intelligence. During their debate, Danvers rejects the Supreme Intelligence and destroys a Kree implant inhibiting her abilities, freeing her to realize her full potential.
Danvers defeats Starforce in the following combat, while the others assist the Skrulls in their escape. Goose is revealed to be the Kree extraterrestrial Flerken, and he consumes the Tesseract. Kree warriors led by Ronan the Accuser arrive to assist in defeating the Skrulls but depart when Danvers destroys an entire starship. Danvers defeats Yon-Rogg on Earth and returns him to Hala with a warning for the Supreme Intelligence.
Leaving Fury with a modified pager to reach her in case of emergency, She also asks Fury to keep the tesseract on Earth. Danvers travels to assist the Skrulls in finding a new home world. Meanwhile, Fury loses his left eye after being scratched by Goose. While recovering, he creates a program to find heroes like Danvers and names it after her Air Force call sign, "Avenger." In the present day, Fury activates the pager, which is being monitored by the Avengers as Danvers appear. Goose throws up the Tesseract on Fury's desk.
