On board the cruise ship they celebrate their 700 years in space, on their expected 5-yr voyage. Everyone is grossly overweight due to the effects of gravity and a lifestyle where their every need is catered for by robots. Makes you wonder how they have babies in the nursery - but its a Disney movie, so we don't go there.
EVE gives the plant to the Captain, and the re-colonization plan is put into effect. The Captain looks through the logs to find out more about Earth. Meanwhile, EVE is cleaned up - but WALL-E mistakenly assumes she is being harmed - and in helping her only breaks out other, damaged robots.
EVE puts WALL-E on an escape pod to send him back to Earth so he can do no more harm - but WALL-E is not alone, as the little GOFER robot drops the boot holding the plant inside the pod and it is jettisoned - and set to self-destruct.
WALL-E breaks out, with the boot, before it blows and - using a fire extinguisher with an impossibly huge amount of gas - flies back to the ship and dances through space with EVE.
EVE and WALL-E make it back to the Captain's quarters - but find out that the Auto Pilot is the bad guy - responding to an over-riding directive never to return to Earth. EVE and WALL-E are dropped down the garbage chute, and WALL-E is in bad shape, but they are rescued and helped by the bigger WALL-E robots.
The Captain fights back against the Auto-Pilot, and directs the robots to the central deck with the container that needs the plant that will send the ship back to earth. The Auto Pilot turns the ship around, sending all the fatties sprawling against the side windows and the plant device starts to close. WALL-E hurls himself into the machine to keep it open, badly damaging himself, and they manage to get the plant inside before it closes.
The ship enters hyperspace back to Earth.
When it lands, EVE rushes WALL-E back to his little truck and fixes him up - but his memory has been wiped. She holds his hand and gives him an electric kiss, which reboots his system, and the other damaged robots celebrate.
The Captain teaches everyone how to care for the plant in the boot - but just over the hill we see that many more shoots have started to grow.
In the credits we see the humans starting to care for their world again.