Theseus

A friend and an enemy to the crew of the Phoenix-X, Admiral Theseus put the Phoenix-X's launching in motion and had all the Starfleet paper-work done. For a while he was the fore-runner in handing out missions to the Phoenix-X, until Section 31 took over a more prominent role. (PNX: "The Tiloniam System")

Theseus works closely with Section 31 on many secret goals. He often uses Admiral Cloud to do his bidding, his possibly tracible dirty work, and then has Cloud's memory erased illegaly. (PNX: "Killing Spree")

There may be a good chance that Theseus is actually an all-knowing and powerful alien, although this is merely speculation so far. (PNX: "Guinea Pigs")