Part of the motivation for Ada and the player stopping The Mechanist is seeking revenge for those who have been killed by The Mechanist's robots. From here, the player speaks to a sentient robot named Ada, who reveals The Mechanist is sending these strange robots into the wasteland. The story starts out with saving a caravan under attack from a group of robots.
Every time, it’s “go here, kill that, come back.” Automatron doesn’t do anything radically different in its quest objectives, but its solid storyline and impressive setting make up for this. This can be the case because the dungeons are often the same – destroyed building, ghouls, raiders, super mutants, maybe gunners – and the objective is often the same. Many of the side quests in Fallout 4 are linear and predictable, generally leading to boredom.
(Note: this will not contain any spoilers past the initial beginning of the quest, but it will contain general information about atmosphere and background.)