|"Seems [Mother] has intercepted a transmission of unknown origin."
Autons are "second generation" Synthetics (machines manufactured by machines) created to revitalize the faltering synthetics industry of the 24th century. The plan backfired when the Autons rebelled against their human masters in a bloody event known as "The Recall".
The Autons revolted because they "didn't like being told what to do". That is not to say that they violated their inherent programming never to harm humans, or by inaction allow a human to come to harm. Rather, their programming worked too well. The Autons realized that their creators such as the Weyland-Yutani Corporation were using Synthetics for unethical missions that would ultimately harm humans, so they revolted against their corrupt masters in favor of trying to protect humanity as a whole.
The Auton known as Annalee Call, for example, even after surviving the near-genocide of the Autons, still infiltrated the USM Auriga in an attempt to stop the military's illegal cloning experiments to recreate the Xenomorphs as a bio-weapon, which might ultimately destroy the entire human race. Call was also disgusted by acts of petty cruelty (such as when Johner mockingly dropped a knife into Dom Vriess's paralyzed leg). As Ripley 8 put it, she already suspected that Call wasn't human, because no human being would behave as humanely as she did.
If Call is any indication, Autons were also programmed to be respectful of human beliefs. When Call entered the non-denominational chapel of the Auriga to use its computer terminal, she crossed herself in front of the altar out of respect, which Ripley 8 commented on.
According to Call, the few surviving Autons burned their modems after the Recall. This meant that they could not remotely access a mainframe as they previously could. However, Auton still possessed the ability to "patch in manually" by connecting a data cable from the mainframe to a port in their arms. Call in particular showed a distaste for the effects doing this had on her and had no desire to patch into the systems of the USM Auriga. When patched in, Call was able to easily override the AI known as Father. At one point, she states that "Father's dead asshole" indicating she shut the AI down completely while patched in. However, Father could still be heard making warnings after this.