Vigil

In his own words, Vigil is a "Advanced non-organic analysis system with personality imprints for Ksad Ishan, chief overseer of the Ilos research facility."
=== Description ===
It seems likely that originally, Vigil appeared to be a holographic prothean, much like "Victory", the prothean VI who oversaw Javik's project.
By 2183, when he spoke to Commander Shepard, Vigil's appearance was closer to angry orange lines of static, wrapping around themselves in a neon tangle. No humanoid-like features were seen.
=== History ===
==== Fallen Empire ====
At the height of the Prothean Empire, the Reapers struck. Using the Citadel's function as a mass relay to dark space, the machines decimated the heart of prothean civilization and quickly learned everything there was to know about the organics.
Almost everything. In the initial attack, all references to Ilos and it's top-secret research facility were destroyed. Those on the planet retreated deep into the bunker and cryogenically froze themselves, hoping to remain unnoticed until the danger passed.
To facilitate this, using their chief overseer's personality imprints, they created Vigil and charged him with monitoring the facility and to waking those in cryosleep when the danger had passed.
Unfortunately, the Reapers took centuries in hunting down all protheans throughout the galaxy. The power that was required for the crygenic pods operation began to wane. This possibility was one of many that had been accounted for in Vigil's programing, and following out his instructions he began to shut down the pods of the non-essential employees to conserve energy. Eventually, only the top scientists' pods remained active, though the power situation was bad enough that they were in danger of failing. When the Reapers retreated back into dark space, Vigil woke those who remained- roughly a dozen individuals. They immediately realized that they were likely all that was left, and the prothean race was doomed.
The first thing they did was sent a message along the beacon network. They had little hope of it being received anywhere with the likelihood that the extinction had destroyed any working beacons left, not to mention the possibility of being discovered by any Reaper or Reaper forces left behind. Still, they sent the message with the hope if any of their people were left alive, they would know of Ilos, it's researchers, and feel hope. Then, they set their minds to stopping the Reapers from returning. And they knew the key was the Keepers.
It took decades of frantic experimentation and study, but at last they discovered a signal sent to the Keepers to activate the Citadel and bring the Reapers from dark space and a way to alter the signal. Using the Conduit, a functional miniature mass relay connected to the Citadel and a product of their earlier research, they traveled to the Citadel and implemented the change needed. Vigil did not know what happened after they left, but they appeared to be successful- though Vigil 'feared (the scientists) suffered a grim fate' due to the probable lack of food and water on the deactivated Citadel.
Vigil himself went into stasis, his job done, and a long silence settled over Ilos.
=== Shepard and Saren ===
Sometime around August of 2183, rogue Spectre Saren Arterius, with the Cypher in his mind and the co-ordnates of the Mu Relay in hand made the journey from his base on the planet Virmire with his geth army to the planet Ilos. Hot after him was Commander Shepard, who had stole the Normandy to pursue him.
Vigil detected their presence and monitored their communication. It is unclear if Vigil refused to speak to Saren after the VI detected indoctrination, if Vigil did speak to Saren, if Saren never found Vigil, or if Vigil only powered up after Shepard restored power to the base. As Shepard, Liara, and Garrus descended downward, Vigil activated barriers to stop the squad and direct them towards him. Once they arrived, Vigil told the three of them about the Coduit, the Keeper signal, and what little he knew of the Reapers and the fall of the Prothean Empire and those at Ilos. He provided a data file to the group of them to give Shepard temporary control of the Citadel's functions. Vigil shut down shortly afterward due to the damages of time and lack of power. 
=== A Shadow Game ===
Vigil remained offline for just over five years, completely escaping the notice of the salarians who came after Ilos' rediscovery for study in 2134-6, though it seems that Ilos was abandoned when the Reaper war started. Liara also travled to Ilos on multiple occasions during this time, though the first time she arrived, there was inadequate power for Vigil to activate (and the following times Liara did not require his assisitance). On September 27, 2188, the slow trickle of power from the solar panels installed by Liara had given Vigil enough to activated when a strange man arrived on Ilos. This individual did not register as any known type of sapient to Vigil's sensors, so Vigil activated to address him. The man had questions, or rather, one question in particular: “I need to know… where it began.” Vigil provided data on " historical information on the Reapers, particularly data regarding previous cycles", but the man wished to know more. Vigil then directed him to the cache of inusannon technology below the prothean base. Afterwards the man disappeared and did not reappear on any of Vigil's sensors, though he returned with other companions later and cleared away the geth bodies left from Saren's landing years prior.
On November 30, 2188, Shepard returned to Ilos and was shocked to discover Vigil was active and was disquieted to hear about the mysterious person with their questions and Vigil's inability to see them. After asking what data this individual accessed, Vigil directed Shepard, Garrus, Liara, and Vega deeper into the darkness of the base.