In the 29th century, Earth has become a garbage-strewn wasteland due to rampant consumerism and corporate greed; seven centuries earlier, the megacorporation Buy-n-Large (BnL) evacuated humanity to space on giant starliners. Of all the trash compacting robots left by BnL to clean up, only one remains operational, Waste Allocation Load-Lifter: Earth-Class (WALL-E). One day, WALL-E's routine of compressing trash and collecting interesting objects is broken by the arrival of an unmanned probe carrying an egg-shaped robot named Extraterrestrial Vegetation Evaluator (EVE). She has been sent to scan the planet for signs of sustainable life. WALL-E is smitten by the sleek, otherworldly robot, and the two begin to connect, until EVE goes into standby when WALL-E shows her his most recent find; a living seedling. The probe then collects EVE and the plant, and, with WALL-E clinging on, returns to its mothership, the starliner Axiom.

In the centuries since the Axiom left Earth, its passengers have degenerated into helpless corpulence due to laziness and microgravity, their every whim catered to by machinery. Even the captain, B. McCrea, is used to sitting back while his robot steering wheel AUTO flies the ship. McCrea is unprepared to receive the positive probe response, but discovers that placing the plant in the ship's Holo-Detector will trigger a hyperjump back to Earth so humanity can begin recolonization. When McCrea inspects EVE's storage compartment, however, the plant is missing, and EVE blames WALL-E for its disappearance.

EVE is deemed faulty and taken to Diagnostics. Mistaking the process for torture, WALL-E intervenes and releases all the other faulty robots in the process, causing him and EVE to be designated as rogues. Frustrated, EVE tries to send WALL-E home in an escape pod, but they witness AUTO's gopherbot GO-4 stowing the plant in a pod set to self-destruct. WALL-E enters the pod in an attempt to retrieve the plant, but is then launched into space along with it. EVE then uses an emergency exit to chase after WALL-E, and witnesses the pod explode. WALL-E survives and saves the plant, and he and EVE reconcile, celebrating with a dance in space around the Axiom.

EVE brings the plant back to McCrea, who watches EVE's recordings of Earth and concludes that they have to go back to save it. However, AUTO has been programmed with the secret never-return directive A113—issued after BnL incorrectly concluded in 2110 that the planet could not be saved. When McCrea countermands the directive, AUTO and GO-4 mutiny, electrocuting WALL-E's circuit board, putting EVE into standby, throwing them both down the garbage chute, and locking McCrea in his quarters. EVE and WALL-E are nearly ejected into space along with the ship's trash, but a Microbe Obliterator (M-O) has been following WALL-E's dirt trail across the ship, and inadvertently alerts the other robots that WALL-E and EVE need rescuing. As humans and robots help in securing the plant, McCrea and AUTO fight for control, resulting in WALL-E being crushed by the Holo-Detector while trying to keep it open; McCrea eventually overpowers and deactivates AUTO, and the plant is inserted into the Holo-Detector, initiating the hyperjump.

Arriving back on Earth, EVE repairs WALL-E, but finds that his memory and personality have been erased. Heartbroken, EVE gives WALL-E a goodbye "kiss", which sparks his memory and restores his original personality. WALL-E and EVE reunite as the inhabitants of the Axiom take their first steps on Earth. During the credits, humans and robots turn the ravaged planet into a paradise, and the plant is shown to have grown into a mighty tree, which EVE and WALL-E rest beneath.