One day WALL-E discovers a growing seedling. Later, a spaceship lands and deploys EVE, an advanced robot probe sent from the BnL starliner Axiom to search for vegetation on Earth. WALL-E falls in love with the initially cold and hostile EVE, who gradually softens and befriends him. When WALL-E brings EVE to his truck and shows her his collection, she sees the plant, automatically stores it inside herself, and goes into standby mode waiting for her ship to retrieve her. WALL-E, not understanding why EVE seems to have shut down, tries numerous methods to reactivate her, to no avail. When EVE's automated ship returns and collects EVE, WALL-E clings to its hull and thus travels through space back to the Axiom, which is hidden behind a nebula.
On the Axiom, the descendants of the ship's original passengers have become morbidly obese after centuries of relying on the ship's automated systems for their every need. The ship's 6th captain, McCrea, leaves most of the ship's operations under the control of its robotic autopilot, Auto.
WALL-E follows EVE to the bridge of the Axiom, where the Captain learns that by putting the plant in the ship's holo-detector to verify Earth's habitability, the Axiom will make a hyperjump back to Earth so the passengers can recolonize it. However, Auto orders McCrea's robotic assistant GO-4 to steal the plant as part of his own no return directive, which was issued to all BnL autopilots after the corporation incorrectly concluded in 2110 that the planet could not be saved.
With the plant missing, EVE is considered defective and taken to the repair ward along with WALL-E (for cleaning). WALL-E mistakes the process on EVE for torture and tries to save her, accidentally releasing a horde of malfunctioning robots. The on-board security systems then designate both WALL-E and EVE as "rogue robots". Angry with WALL-E's disruptions, EVE brings him to the escape pod bay to send him home. There they witness GO-4 dispose of the missing plant by placing it inside a pod which is set to "self-destruct mode". WALL-E enters the escape pod in attempt to retrieve the plant, but GO-4 jettisons the pod into space. WALL-E escapes with the plant before the pod explodes. Reconciling with EVE, they celebrate with a dance in space outside the Axiom.
With the plant brought to the captain, EVE's recordings of Earth are surveyed and concludes that mankind must return to restore their ruined home. However, Auto reveals his directive and stages a mutiny. He tasers WALL-E, severely damaging him, when he tries to protect the plant. EVE realizes the only parts for repairing WALL-E are in his truck back on Earth. She helps him bring the plant to the holo-detector to activate the ship's hyperjump. McCrea opens the holo-detector and fights Auto for control of the ship. Auto partially crushes WALL-E by closing the holo-detector on him. Auto is eventually disabled by McCrea, and EVE places the plant in the holo-detector, which frees a crushed WALL-E and sets the Axiom on the instant hyperjump to Earth.
EVE immediately brings WALL-E back to his home where she repairs and reactivates him. After the repair WALL-E no longer recognizes EVE, reverting to his original programming as an emotionless waste compactor. Heartbroken, EVE gives WALL-E a farewell kiss that jolts WALL-E's memory, and his personality returns. WALL-E and EVE happily reunite as the humans and robots of the Axiom begin to restore Earth and its environment.