Unit E is a secret division of the United States Military tasked with handling special threats to national security. They are thus the primary link between Team Prime's Autobots and the government of the United States of America, and their allies in conflicts against such villains as the Decepticons and MECH. Agent William Fowler is the highest-ranking confirmed member of the unit, and reports to General Bryce. Unit E operates from a military base, specifically from a hanger with the letter E painted on the outside.
- Unit E is reminiscent of human organizations from other Transformers continuities that have worked in tandem with the Autobots, such as the Earth Defense Command of Generation 1 and the N.E.S.T. Taskforce from the Michael Bay films.