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 hangar with the letter E painted on the outside.
Agent William Fowler joined Unit E as a federal agent at least 30 years before he became Team Prime's government liaison. The group's insignia adorns the door to his office.
The agency lent the Autobots a new base when they regrouped after destroying Darkmount. Unit E's mess hall was later destroyed by Starscream, leading the Decepticons to believe they had destroyed the Autobots' base. When Megatron was killed and Cybertron was restored, Team Prime decided to leave Earth to rebuild their home planet. Agent Fowler inducted Jack Darby, Miko Nakadai and Raf Esquivel into Unit E as consultants to defend the Earth. Ratchet also joined the agency to lend Autobot assistance while the rest of the team left for Cybertron.
- 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.