Much like HAL 9000 from 2001, Auto the Autopilot for the Axiom in Wall-E is driven by his main directive to commit atrocities against the passengers of the ship. Yes, he was programmed to carry out Shelby Forthright’s Directive A-113, but like HAL, he also has self preservation in mind.
Thanks to a small detail early in the film, it was clear that the ship's artificial intelligence had its own agenda.
In portraits of past Axiom captains there are hints about the ship, its crew, and its history that are revealed. In addition to the captain growing significantly larger due to the lack of exercise available on the ship, their lifespans are also lengthened by decades. But a key piece of foreshadowing in the portraits is Auto in the background.
With each portrait, Auto inches closer and closer, creeping on the captain as if to gain more control of the ship and its captain. Which is exactly what the AI was doing for years and years. Until finally, Auto almost shares the portrait completely with current leader, Captain B. McCrea.
It is a creepy realization that Auto has slowly been taking over in the last century without anyone's knowledge, but the images are evidence to its evil agenda.