Sovereign

"Random Frieden: Oh great Sovereign, thou art god. We entreat thee with awe, that thou mayest blow thine enemies to little bitty pieces, that thou mayest smite thy foes into a fine, gruel-like paste, that thou mayest explode thy adversies into blossoms of gore and bloody chunks, that thou... Sovereign: STOP WORSHIPPING ME, YOU LITTLE PIECE OF SHIT."

- Sovereign

Sovereign is a Reaper who functions as flagship of the frieden Human Jack Harper, and as such, crewed himself with omar and geth heretics, indoctrinated Friedens, cloned krogan, Myrmidons and indoctrinated Penthesilians. At two kilometers long, his spinal-mounted main gun is capable of penetrating a citadel dreadnought's kinetic barriers with a single shot.

Background
Sovereign is a reaper - a gigantic starship of almost unimaginable power and sophistication housing a fully sentient and extremely powerful AGI, which is why his crew obeys his commands and worship him as a god. The Geth Heretics, for instance, see Sovereign as the pinnacle of AGI evolution. However, Sovereign regards the crew as no more than tools to aid him in the return of the Reapers and is even insulted by the worship his crewmebers at him.

A vanguard of the Reapers left behind to instigate their eventual return from dark space, Sovereign has spent the last 50,000 years in a state of near-constant hibernation, waking periodically to assess the evolution of organic races. It was the duty of the starship to bring about the next revolution of the cycle, and serve as the harbinger for the return of his kind by sending a signal to the keepers on the Citadel. This would make the keepers open the Citadel relay, a mass relay that leads to dark space, and usher the Reapers through.

The Puppeteer
Despite Sovereign's contempt for all organic life, the failure of the signal to activate the Citadel due to Prothean sabotage forces him to investigate what had gone wrong, a task for which he requires centuries of assembling the pieces of the puzzle, working through agents and keeping his true nature hidden, since revealing his presence would have united all organic races against him. Gradually Sovereign pieces together the actions of the last Prothean survivors and discovers the Protheans sent the Shibboleth, a last will and testament for the protean species, through their beacons that might lead it to the Conduit.

When Jack Harper disocvered Sovereign, Sovereign now has the organic ally he needs—a powerful and well-connected Frieden. He makes an alliance with Harper, who thinks he can prove that organics could be useful to the Reapers, guaranteeing their survival when the cycle begins again. Harper doesn't realise that this "alliance" is empty: Sovereign sees him merely as another tool to be manipulated, used, and discarded. Harper takes Sovereign as his flagship, and is named as Sovereign's "prophet" to Harper's sect. However, like so many others, Harper falls under the dominating effects of Sovereign's indoctrination. But he retains some free will, as Sovereign requires Harper's mind intact to find the Conduit and reactivate the Citadel relay. After so many years, Sovereign is finally bold enough—or desperate enough—to begin acting openly.

Quotes

 * SOVEREIGN? FAILURE? IMPOSSIBLE!