The film starts as a fleet of Kree ships finish destroying a planet before passing through a portal known as a jump point. The villains make their way to the moon, where their leader, Dar-Benn (Zawe Ashton), uncovers a vessel containing a Quantum Band, which looks like a familiar bangle. After Dar-Benn learns there is another out there, she wonders would could be in possession of it.
In Jersey City, Kamala Khan/Ms. Marvel (Iman Vellani) is fantasizing about a team-up with Carol Danvers/Captain Marvel (Brie Larson). After a brief moment of geeking out in her costume, her bangle starts to glow. Then, in a flash, Kamala appears to glitch and disappear.
Earlier in the day, Carol, is aboard a ship trying to look into the memories stolen from her by the Kree. She also now takes care of Flerken kitty Goose. Carol is contacted by Nick Fury (Samuel L. Jackson) from his SABER station, who mentions that Monica Rambeau (Teyonah Parris) is working with them to investigate an anomaly. Carol is surprised to hear about Monica, forgetting that she was a child the last time Carol saw her. Carol flies over to the moon and sees the jump point still being opened over a crater on the surface. She finds evidence linking the anomaly to the Kree, specifically Dar-Benn. As this happens, Monica approaches the anomaly with her own powers, which creates an entanglement affecting her, Carol, and Kamala.
Kamala gets switched into Monica’s suit, while Monica ends up on the moon, and Carol crashes into Kamala’s bedroom. While Carol meets Kamala’s family – mom Muneema (Zenobia Shroff), dad Yusuf (Mohan Kapur), and brother Aamir (Saagar Shaikh) – Monica ends up fighting Kree villains storming the moon targeting Carol, calling her “The Annihilator”. Carol gets swapped back into the action and fights them before trying to report to Fury that the Kree are going after Skrulls at their sanctuary on Tarnax. Fury tells them that he is working with both species on peace talks. Meanwhile, Kamala returns home and goes nuts upon learning from her parents that Carol was there, and Monica goes back to Fury after learning that the power switch involved Kamala.
On Tarnax, the Skrull Emperor Dro’ge (Gary Lewis) talks to Dar-Benn, who is working to restore her home world of Hala. She tries to convince Dro’ge that their efforts are working towards reconciliation, but she is trying to get the Skrulls to lower their defenses so she can siphon off the planet’s energy.
The three ladies switch again, with Kamala accidentally grabbing Goose, who had swallowed two Kree goons. The goons then start attacking the Khans and destroying their house while Carol gets switched back to the house so she can fight the henchmen. Kamala ends up on Fury’s station and helps him fight some bad guys while Monica ALSO ends up fighting at the Khan house. After the villains are dealt with, Kamala returns home, and the family is visited by Fury and Monica to explain what is going on. When Kamala tries to demonstrate her powers, she gets switched with Carol. Monica explains their quantum entanglement, so Carol tries to find a way to get Kamala back, only for the teen to end up falling through the sky. Monica, who hasn’t quite mastered her flying abilities, then goes up to save her. They end up on Dar-Benn’s ship and are confronted by the villain and her henchmen.
Before Dar-Benn can kill Monica and Kamala, Carol swoops in and gets them out of there. Dar-Benn then meets everyone on the surface of Tarnax as she begins to set her plan into motion. She opens another jump point that begins to siphon the atmosphere and send it to Hala. The three heroes evacuate the Skrulls and board them onto their ship as Tarnax falls to ruins.
The Kree return to Hala, which has now become breathable once more. Dar-Benn reminds her followers that Carol is responsible for their downfall after she destroyed the Supreme Intelligence, which led to the Kree Civil War that led the planet to its devastation. While she intends to restore Hala’s sun, her second-in-command Ty-Rone (Daniel Ings) warns her that energy from the other Quantum Band is needed, which could destroy her.
Carol contacts Valkyrie (Tessa Thompson) and has her appear via the bifrost so that she can escort the Skrulls to New Asgard for refuge. While Carol expresses some feelings about ending up on a team, Valkyrie assures her it might not be bad for her. After they leave, Carol is met by Monica to fix something on the ship. Monica expresses her own feelings toward Carol over not seeing her for so long. Along with Kamala, Carol tries to track down Dar-Benn using technology that would allow them to see into each other’s memories since Kamala saw a map and coordinates on Dar-Benn’s ship. In that time, Monica sees a memory of her mother Maria (Lashana Lynch) talking to Carol while she was dying from cancer and Monica had gotten blipped. The moment proves too much for Monica, so she breaks the link. Kamala pulls both ladies in for a comforting hug.
Continuing their work, the ladies (unofficially now known as “The Marvels”) determine that Dar-Benn is heading toward the planet Aladna next to siphon their oceans. As they head over there, Kamala learns that her family is being taken care of by Fury, and Muneeba tells Carol and Monica to look after her daughter. Before heading to the planet, the heroes work together to try and get their switching under control.
On Aladna, the inhabitants communicate through song. Carol reveals to Monica and Kamala that she is technically the princess of the people due to helping Prince Yan (Park Seo-joon) out with “legal issues”. Carol talks to Yan and tries to get help from his army in fighting Dar-Benn while trying to protect his people from her attack. A battle ensues once the Kree arrive through jump points, and Yan’s army heads in with him leading them. Carol and Monica cannot properly strike Dar-Benn without their powers glitching. Dar-Benn sees Kamala is in possession of the other band, but fails to catch her. She proceeds to open the jump point that starts absorbing the planet’s water and sending it to Hala. The Marvels then fly away, evading enemy ships before teleporting elsewhere.
Carol tells Monica and Kamala that it’s her fault that everything is happening after she destroyed the Supreme Intelligence, which also caused her enough guilt to not return home to Earth. After the ladies resolve things, they find that Dar-Benn is set to open the last jump point to absorb the sun. They then warn Fury to get everyone at SABER evacuated. Just as this happens, several brain-like eggs that they were studying begin to hatch, revealing a litter of Flerkittens.
The Marvels arrive on the SABER station to help people and use the Flerkittens to swallow everyone and transport them inside their stomachs as they all fit into one evacuation pod. Fury, plus the Khans, get everyone out to safety. The ladies then confront Dar-Benn for a three-on-one showdown, where they all finally keep their powers under control and being to pummel her. One good punch from Carol sends the villain flying into a wall, where she is impaled by falling debris. Carol then tells her she can use her own energy to help restore Hala’s sun. Dar-Benn appears to concede, but when the debris is removed, she attacks Kamala and takes her bangle. Dar-Benn proceeds to tear open a hole in time and space, and the energy from the bands causes her to explode. In order to close the hole, Carol and Kamala each give Monica a burst of their energies so that she can fly over and seal it from the other side of the tear. Monica is left trapped on the other side while Carol and Kamala sadly return to Earth.
Carol fulfills her promise and helps restore Hala’s sun. She later helps the Khans move into the Rambeau’s old house in Louisiana. Kamala then bonds with her idol as they wonder what their next moves will be.
In New York, Kamala uses Fury’s tech to gather intel on Kate Bishop (Hailee Steinfeld). She tries to pull a Fury and recruit her like he did with Tony Stark, setting the stage for the Young Avengers.
During the credits, Monica wakes up in a bed and is met by who appears to be Maria. When Monica addresses her as her mother, Maria doesn’t appear to recognize her. Monica is then met by none other than Hank McCoy/Beast (Kelsey Grammer), who refers to Maria as “Binary”. Monica then finds she is inside the X-Mansion, and Beast states that Charles is asking for updates.