In 1980, Meredith Quill is courted by Ego who shows her an alien seedling he had planted in the woods of Missouri.

Thirty-four years later in 2014, the Guardians of the Galaxy are renowned as heroes after defeating Ronan the Accuser. They accept a job from Ayesha, leader of the Sovereign, to defend valuable batteries from the Abilisk, in exchange for Nebula, whom the Sovereign captured following the Battle of Xandar. After defeating the Abilisk, Rocket Raccoon steals several of the Anulax Batteries for himself, and when the Sovereign discover this, they attack the Guardians' ship, the Milano, with their own fleet of Omnicrafts. The Milano is heavily damaged and forced to crash-land on a nearby planet, but the Sovereign fleet is single-handedly destroyed by Ego, who reveals himself as Peter Quill's father. Ego invites Quill to return to his home, accompanied by Gamora and Drax the Destroyer. Rocket and Groot remain to repair the Milano and guard Nebula.

Ayesha hires Yondu Udonta, who has been exiled from the greater Ravager community for trafficking children, to recapture the Guardians. Udonta's crew track down the Milano and capture Rocket, but when Udonta shows reluctance to turn Quill over to the Sovereign, Taserface leads a mutiny with help from Nebula, who tricked Groot into freeing her. Quill, Gamora, Drax, and Ego, along with Ego’s empathic assistant Mantis, travel to Ego’s home, a living planet that is an extension of his body. Ego explains that he is a Celestial who created a humanoid avatar to travel the galaxy and interact with other species. Quill soon learns he can access and manipulate the power within Ego’s planet. Drax becomes friendly with Mantis, who wants to reveal a secret about Ego.

Taserface imprisons Rocket and Udonta aboard the Eclector and turns Groot into a mascot for the crew, while Nebula takes a ship and leaves, planning to track down and kill Gamora, blaming her for the torturous cybernetic enhancements inflicted by her father Thanos. In their imprisonment, Rocket and Udonta discover they are very alike, and Udonta shares his low opinion of Ego, who originally hired Udonta's Ravagers to deliver Quill after his mother’s death. He reveals to Rocket that he decided to keep Quill safe in his own way, instead of handing him over to Ego. Groot attempts to steal a new Yaka Arrow Controller for the Yaka Arrow to aid an escape attempt, and is helped by Kraglin Obfonteri, a Ravager loyal to Udonta. Together, Rocket, Groot, Udonta, and Obfonteri escape in a detachable section and engage in a risky space maneuver to reach Ego's planet in time to help Quill. Taserface alerts the Sovereign of the escape before Udonta kills him and the Ravager mutiny.

Nebula arrives at Ego’s planet and tries to kill Gamora. Gamora survives and reaches an uneasy truce, and together, she and Nebula explore the caverns beneath Ego’s planet and discover hundreds of skeletal remains. Ego reveals his master plan to Quill: he traveled the universe and, finding the life-forms he found 'disappointing', he planted seedlings on thousands of worlds that would terraform them into new extensions of Ego, but he needed a second Celestial’s power to activate the seedlings, so he conceived children with hundreds of women all across the galaxy and hired Udonta's Ravagers to collect them. Every other child was killed when they proved unable to access Celestial power, but Quill can harness the power, and Ego uses him to activate all the seedlings, which begin their terraforming that will eventually consume every world and every person. Quill is hypnotized by Ego’s power until Ego reveals he deliberately caused the death of Quill’s mother, prompting Quill to fight back.

Mantis informs Gamora, Drax, and Nebula of Ego’s plan just as Rocket, Groot, Udonta, and Obfonteri arrive. Reunited, the Guardians fight their way through a fleet of Sovereign drones, as well as Ego himself, to reach the core of Ego’s planet where a thick shell protects the Ego's brain. Groot plants a bomb made from the stolen Sovereign batteries on Ego’s brain, and most of the Guardians escape while Quill remains to battle his father using his access to Ego’s celestial power. When the bomb explodes, Ego melts away and the planet starts collapsing. Udontaflies in and saves Quill, but sacrifices himself to keep Quill safe, as he has come to view him as an adopted son. Later, Nebula reconciles with Gamora but chooses to leave to kill Thanos anyway. The Guardians cremate Udonta's remains and release his ashes into space. Suddenly, a swarm of Ravager ships appears and surround the Guardians' ship. It turns out that Rocket sent word about Udonta's sacrifice and all the Ravagers came to perform a traditional Ravager funeral for Udonta, signifying his acceptance back into the Ravagers.

Afterwards: Obfonteri takes up Yaka Arrow and controller and tries to master it, only to end up non-fatally impaling Drax; Stakar Ogord is moved by the death of Udonta, his good friend and former teammate, and reunites with his former teammates Charlie-27, Aleta Ogord, Mainframe, Martinex and Krugarr; Ayesha, now imprisoned by her fellow Sovereign for wasting resources in her hunt for the Guardians, is seen with a Birth Pod, containing a male being inside, that she decides to name 'Adam', in response to her fellow Sovereign questioning her about said machine; years later, Groot continues growing back to normal size, exhibiting typical teenage behavior in the process; to Quill's chagrin; and the Watcher Informant discusses his experiences on Earth along with a group of Watchers.