A set of command routines added to Voyager's Emergency Medical Hologram that allow the Doctor to take charge of the ship if the captain and senior officers are lost or incapacitated.
The Emergency Command Hologram, or ECH, begins as the Doctor's own proposal. In the Voyager episode Tinker, Tenor, Doctor, Spy he asks Captain Janeway to let him serve as a backup commander, and daydreams about it, complete with a red uniform and four pips.
Aliens of the Hierarchy tap into those daydreams and mistake them for fact. When they attack, the Doctor has to play the part for real, bluffing them with a non-existent photonic cannon. Janeway agrees to look into the idea afterwards.
By Workforce the routines exist. The crew are abducted to work on Quarra and the Doctor is left to run Voyager as ECH, defending and repairing it with only Chakotay, Kim and Neelix to help. He uses the same authority, less nobly, in Renaissance Man.