Sovereign

Sovereign is the flagship of the rogue Spectre Saren. 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. Sovereign has a distinctive organic design, looking somewhat like a giant cuttlefish.

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.

How Saren acquired this incredible warship is unknown. The prevailing opinion is that Sovereign is a geth construct, while others believe it is a Prothean relic.

(Source: in-game Codex)

 "I am the vanguard of your destruction."

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 a Reaper itself, 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 the geth as no more than tools to aid in the return of the Reapers, and Saren as simply a useful slave. 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 spider-cuttlefish-scorpion-esque starship to bring about the next revolution of the cycle, and serve as the harbinger for the return of its kin by sending a signal to the keepers on the Citadel. This would make the keepers open the mass relay that led 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 husk 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."

Discovery
Sovereign was discovered in 2162 by one of Edan Had'dah's survey teams, which was exploring near the Perseus Veil. Had'dah was a batarian entrepreneur who sent teams out to find ancient alien technology, usually Prothean, and either sold or researched it for profit. But when his people reported their find, Had'dah soon realised he had something unprecedented on his hands. Had'dah quickly isolated the survey team on a nearby planet and searched for an expert who could help him unlock Sovereign's secrets. He eventually found Dr. Shu Qian, whose defection from the Alliance sparked the events of Mass Effect: Revelation.

But Sovereign's indoctrination effect was already working on Qian. Even a brief visit to the 'artifact' also affected Had'dah's mind, until the two were obsessed with researching the ship. During his investigation, Saren Arterius became intrigued by what he heard, wondering if Sovereign was the weapon he had been looking for to bring humanity to its knees. He killed both Qian and Had'dah and took their research, then went to find Sovereign of his own accord.

Mass Effect
Though Sovereign views all organic life as expendable and merely a means to an end, after the signal to the Citadel failed to work thanks to the Protheans' sabotage, it was forced to work through a series of thralls to gain access to the station, because revealing its presence would have united all organics against it. Somehow Sovereign pieced together the actions of the last Prothean survivors and realised the Protheans had sent a final message through their beacons that might lead it to the Conduit.

It eventually struck a deal with Saren, who thought he could prove that organics could be useful and guarantee their survival when the Reapers returned. But Sovereign merely saw him as a tool to be used and discarded. Saren took the great machine as his flagship, only to later fall -- like so many others -- under the dominating effects of Sovereign's indoctrination to carry out its plan. However, Sovereign required him to have his mind intact to reactivate the Citadel relay. Vigil claims Sovereign may have been planning this strategy for centuries, working behind the scenes, and only now grown bold enough - or desperate enough - to act openly.

When a Prothean Beacon was unearthed on Eden Prime, Sovereign realised it might contain the location of the Conduit but was unable to access the vision itself, as it was coded so only organic minds could understand it. Sovereign brought Saren and an army of geth to the colony to retrieve the beacon. Eden Prime was devastated in the assault, not only from Sovereign's weapons but its engines, which burned crops for miles around. However Sovereign's presence was transmitted by the marines on the surface before they were killed, alerting the SSV Normandy. Nonetheless, after Saren used the beacon, Sovereign learned more about the Conduit, a reverse engineered mass relay made by the Protheans, designed as a backdoor onto the Citadel.

Sovereign eventually returned to Virmire, where Saren had built a base and breeding facility for his krogan army. The base was attacked by Commander Shepard, who used another beacon in Saren's communications lab and alerted Sovereign to the commander's presence. It spoke to Shepard directly, expressing its disdain for organic life and claiming Shepard's attempts to stop the Reapers from returning were futile. Sovereign then attempted to reach Shepard's position on the surface, but Shepard destroyed the base and escaped in the Normandy before Sovereign arrived. The encounter with Shepard left Saren with doubts about the Reapers eating away at his loyalty to Sovereign, so Sovereign implanted him with cybernetics to control and fully indoctrinate the turian.

With the help of Shiala and Matriarch Benezia - other victims of Sovereign - Saren finally found the Conduit on Ilos. He travelled through it to the Citadel with a small army of geth and took control of the station from within. Meanwhile, Sovereign led a huge armada of geth to attack the Citadel Fleet. Saren closed the Wards around Sovereign while it began using the Citadel Tower to override the station's controls and manually open the relay to dark space.

However, Shepard's squad had followed Saren and fought toward Sovereign's position through the Citadel. Saren said that Sovereign was impressed by Shepard and asked the commander to join the Reapers "and experience a true rebirth". If Shepard has enough Charm or Intimidate, Saren can be convinced that the Reaper is controlling him through his implants and commits suicide.

When Saren failed to stop Shepard and died, Sovereign created an avatar through the mechanical implants in Saren's cadaver, and entered a brief but chaotic struggle with Shepard and the squad inside the Citadel Tower. Upon the destruction of that avatar, and under constant bombardment by a full armada of Systems Alliance starships, Sovereign was obliterated, averting the return of the full Reaper fleet from beyond the galactic rim, and saving sentient life from utter destruction. Despite the relief of the Council, Shepard recognized that Sovereign was only a vanguard, and that the rest of the Reapers were still waiting to return eventually.

Trivia

 * Sovereign's spacecraft/squid appearance echoes certain elements of H.P. Lovecraft's Cthulu mythos. In Lovecraft's stories, Cthulu was traditionally described as an omnipotent creature with squidlike features that presumably dwelt in outer space.  Sovereign and Cthulu both share the same appearance, are presumably near-invincible, and have a cult following in their respective stories.