Sovereign

Sovereign, also known as Nazara, 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.

Sovereign is voiced by Peter Jessop.

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 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 is even insulted by the worship the geth "throw" at it, 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 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."

Discovery
In 2162, one of Edan Had'dah's survey teams discovered Sovereign orbiting an uncharted world in an obscure star system 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 the 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.

The Puppet Master
Saren found Sovereign to be not only sentient, but attentive. Though Sovereign viewed all organic life only as a means to an end, after the signal to the Citadel failed after the Prothean sabotage, it was faced with discovering what had gone wrong, and needed organics to help it. Vigil hypothesised it took many years—possibly even centuries—for Sovereign to assemble the pieces of the puzzle, working through agents and keeping its true nature hidden, since revealing its presence would have united all organic races against it. Gradually Sovereign pieced together the actions of the last Prothean survivors and discovered the Protheans had sent a final message through their beacons that might lead it to the Conduit.

When Dr. Qian's research finally led Saren to the planet it was orbiting, Sovereign now had the organic ally it needed—a powerful and well-connected Spectre. It made an alliance with Saren, who thought he could prove that organics could be useful to the Reapers, guaranteeing their survival when the cycle began again. Saren didn't realise that this "alliance" was empty: Sovereign saw him merely as another tool to be manipulated, used, and discarded. Saren took Sovereign as his flagship, and was named as Sovereign's "prophet" to the geth, only to fall, like so many others, under the dominating effects of Sovereign's indoctrination. But he retained some free will, as Sovereign required Saren's mind intact to find the Conduit and reactivate the Citadel relay. After so many years, Sovereign was finally bold enough—or desperate enough—to begin acting openly.

When a Prothean Beacon was unearthed on Eden Prime, Sovereign knew it might contain the location of the Conduit. As a machine it was unable to access the vision itself, as the Prothean message had been 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, which could function as a backdoor onto the Citadel.

Continuing the Cycle
Sovereign eventually returned to Virmire, where Saren had built a base and breeding facility for his krogan army. The base was attacked by 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's indoctrination—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.

The Fall of the Vanguard
However, Shepard's squad had followed Saren and fought toward Sovereign's position through the Citadel. Saren offered the commander the chance to join the Reapers "and experience a true rebirth". When Saren failed to stop Shepard and died (either in a battle to the death with Shepard, or by committing suicide), Shepard then managed to input a data file made by Vigil to temporarily prevent Sovereign from gaining full control of the Citadel.

However, Sovereign created an avatar through the mechanical implants in Saren's cadaver, and attempted to destroy Shepard and the squad inside the Citadel Tower, simultaneously devastating the Alliance Fifth Fleet in the space battle outside. Upon the destruction of its avatar, and under constant bombardment by a full armada of Systems Alliance starships, Sovereign was finally destroyed by a fatal shot from the Normandy, 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.

Mass Effect 2
It is stated by Legion that the name the Reaper used to identify itself originally was Nazara (although it would still address itself as Sovereign to beings that know it as such). Legion describes how 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 species, culture, or "nation."

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.

Trivia

 * Sovereign's spacecraft/squid appearance echoes certain elements of H. P. Lovecraft's Cthulhu mythos. In Lovecraft's stories, Cthulhu was traditionally described as an omnipotent creature with cephalopod features that presumably came from outer space. Sovereign and Cthulhu both share the same appearance, are presumably near-invincible, are stated to be beyond human understanding, are capable of driving people insane with their presence, and have a cult following in their respective stories. The role they play to the others of their kind is similar as well, waiting until the time is right to awaken their slumbering brethren.
 * Sovereign proclaims during the discussion in Saren's lab that "We are legion." This is possibly a reference to a well-known Biblical event of the Gerasene Demon (also referenced as the Gadarene Demon), describing itself as a malevolent gestalt of several malignant entities. The actual quote is: "My name is Legion, for we are many".
 * According to The Art of Mass Effect, features of an insect's anatomy were added to Sovereign's design to further tie it to the geth and the other synthetic species in Mass Effect.