Sovereign

Sovereign  is the flagship of the rogue Spectre Saren Arterius. An enormous dreadnought larger than any other ship in any known fleet, Sovereign is crewed with both geth and krogan. At two kilometers long, its spinal-mounted main gun is likely capable of penetrating another dreadnought's kinetic barriers with a single shot.

The prevailing opinion is that Sovereign is a geth construct, while others believe it is a Prothean relic. Its design, however, hints at a more alien and mysterious origin. The attack on Eden Prime demonstrated Sovereign's ability to generate mass effect fields powerful enough to land on a planetary surface. This implies it has a massive element zero core, and the ability to generate staggering amounts of power.

Overview
Sovereign is a gigantic starship of almost unimaginable power and sophistication. Commander Shepard originally believed Sovereign was a Reaper vessel that Saren Arterius found and somehow reactivated, but discovers Sovereign is in fact an actual Reaper, a fully sentient and extremely powerful AI, which is why the geth obey its commands. They see Sovereign as the pinnacle of AI evolution and worship it as a god. However, Sovereign regards Saren and the geth as no more than tools to aid in the return of the Reapers and is even insulted by the worship the geth "hurl" at it. 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 its 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.

Sovereign is also able to control organic life through the process of indoctrination. A subtle field or signal surrounds the Reaper, gradually affecting the organic's mind until they are little more than a shell of their former self, bent on doing Sovereign's will. Sovereign has nothing but contempt for any lesser beings, seeing them as fleeting and temporary, whereas the Reapers are eternal. It also seemed angered by the attempts of organic life to defend their claim to the Citadel, claiming "this station is mine."

Mass Effect 2
After its destruction, most of Sovereign's debris rained down on the Wards. Between rescue workers looking for survivors and the keepers cleaning up the mess, little of Sovereign's technology could be studied. Some turian researchers discovered that Sovereign's main gun used an electromagnetic field to fire a stream of molten metal at a fraction of the speed of light. These turians reverse-engineered their own version soon after, dubbed the Thanix Cannon. However, what remained was not enough to convince the Council that Sovereign was anything more than a geth construct. Some pieces were recovered by Cerberus to fit into the AI onboard the new Normandy, to use as anti-Reaper algorithms.

It is also implied that Sovereign (or another Reaper operating under the same objectives) was responsible for indoctrinating the rachni queens, resulting in their overly aggressive response to Citadel scout teams and causing the Rachni Wars.

If Legion is activated and allowed to stay on the Normandy SR-2 in 2185, it provides additional information regarding Sovereign. Legion states that Sovereign identified itself to the geth with the name Nazara and that the title 'Sovereign' was coined by Saren, although it would still address itself as Sovereign to beings that know it as such. Legion describes that Sovereign had been searching for allies for over a millennium in order to bring about the cycle once more, and also provides some insight into some of the more enigmatic statements made by Sovereign on Virmire, such as "We are each a nation," referring to how both the geth and Reapers have numerous AI processes running in the same physical construct (possibly many more in the case of the Reapers). The quote is put further into perspective when the nature of Reaper construction is revealed aboard the Collector base, when it is discovered that each Reaper is constructed from the genetic material of a particular sentient race - a "nation."