Like the ancient human city of Troy, Ilos is a world known only through second-hand sources. References to Ilos have been found at several other Prothean ruins, though direct study of the world is unlikely to occur.
Ilos lies in a remote area of the Terminus Systems only accessible by the legendary Mu Relay. Four thousand years ago, the Mu Relay was knocked out of position by a supernova and lost. Since then, Ilos and its cluster have been inaccessible.
Occasionally, a university will organize an expedition to chart a route to Ilos using conventional FTL drive. These never get beyond the planning stages due to the distance and danger. The journey could take years or decades, passing through the hostile Terminus Systems and dozens of unexplored systems.
In the golden age of the Protheans, Ilos was a verdant world, dotted with the spires and arches of magnificent cities. Even casual observation shows this is no longer the case. Ilos has been devastated by means unknown, its entire surface changed to the color of rust. The atmosphere shows heightened levels of oxygen. Wildfires, presumably ignited by lightning strikes, can be seen burning on the dark side. This indicates that most - if not all - respirating animal life forms have died off.
During the prothean reaper war 50,000 years ago, a bunker was created on Ilos that was used to house specialists and scientists of the highest importance. It was a top secret project to begin with, and all official records of the prothean presence on Ilos was destroyed in the initial attack on the citadel. When the prothean empire came crashing down, Ilos was spared. The facility went dark in order to avoid detection and the staff agreed to go into stasis, hoping the danger would soon pass. Vigil, a VI, was assigned to watch over these Protheans in cryogenic stasis until the Reapers had gone, then wake the staff so they could begin to rebuild. But as the centuries passed and the Reapers persisted in their genocide of the Protheans, Vigil's power supplies began running low, and the cryo pods were in danger of failing.
Following contingency planning, Vigil began cutting power to the pods of non-essential staff to conserve energy. When the Reapers finally withdrew through the Citadel relay, only the top researchers — a dozen individuals — were left. Vigil woke them, and the scientists pieced together what had happened.
They soon realised the situation was dire. Without sufficient numbers to sustain a viable population, the Prothean species was doomed. Desperate for contact with others of their kind, a carefully-coded signal was sent to the beacons on other planets. Though it was unlikely there were other survivors, the scientists thought it was worth the risk to try reaching them. The signal not only contained a warning of the Reaper invasion, but a description of Ilos itself, to give them hope.
The surviving Prothean scientists knew that rescue was unlikely. Instead, they chose to protect the races they had been studying, spared destruction due to their lack of advancement, and began working out where the Reapers had come from, and how. After decades of study, they worked out the connection between the Reapers, the Citadel, and the keepers, and discovered a way to interfere with the signal that compels the keepers to activate the Citadel relay. Using the Conduit, the Prothean scientists left Ilos, travelled to the Citadel and altered this signal. Their intention was to prevent the Reapers from opening the Citadel relay again, and trap them in dark space, but they had no way to be certain their plan had succeeded.
The fate of these Prothean scientists is unknown. As the Conduit portal only links one way and there was no food or water left on the Citadel, Vigil hypothesized they eventually starved to death.