AUTO, Take the Wheel
Like half of Twitter, the Axiom is run by robots. It's even guided by a robot, the autopilot Captain's wheel, named AUTO. We actually see AUTO, the captain's wheel, before we see the captain, who is asleep when EVE arrives with the plant.
AUTO tries to prevent EVE from returning the plant to the holo-detector and send the Axiom back to Earth. He goes as far as electrocuting WALL-E to stop them, and his STEWARD-BOTS knock people over, the people they're supposed to be serving, to get to EVE. Plus, his little sidekick bot, GO-4 ("Go for," get it?) is kind of creepy, doing AUTO's bidding and hissing like a rabid animal at robots or humans that get in his way. (GO-4 is one of the only characters to "die" in WALL-E, getting knocked from the Captain's Bridge and exploding on the ground below.)
But despite how despicable his actions are, we hesitate to call him the film's bad guy… even though he's a dead ringer for Hal, the evil robot from 2001: A Space Odyssey. Like all the robots in this story, AUTO has a directive: Directive A113, initiated by the Buy N Large CEO, to prevent the Axiom from returning to Earth.
In the 700 years since that directive was activated, though, things have changed. AUTO's biggest failure is that he lacks critical thinking or the element of choice, features that WALL-E, EVE, and even M-O seem to possess. AUTO runs on autopilot, unable to deviate from the course, and the Captain ends up overpowering him as a result.