The Protheans were the last race to inhabit the galaxy before the Reapers last purge of life. They are highly looked upon in modern galactic civilization in the Mass Effect universe having thought to have created the Citadel, and the Mass Relays, which are the basis of Galactic Civilization. However, a shocking revelation by Commander Shepard and his crew revealed that the Reapers were in charge of constructing all the relics that civilization relies on. Even then, not many believe in Shepard and the Protheans are still held in high regard.
The Protheans are even the basis of some species' religion. The Hanar know them as "The Enkindlers," and view them as their gods. The Hanar attribute their sentience and language to the Protheans and often have peaceful protests at Prothean relics in a bid to preserve them. Throughout the Mass Effect franchise relics can be found on alien worlds, many of these resembling giant glass balls or pyramids, and all evidence shows that they were a highly advanced race, who spanned control over much of the known galaxy. Even then, not much is known about their physiology, however some Protheans have been genetically modified into the main antagonists of Mass Effect 2, the Collectors.
By the time the Reapers activated the Citadel, so the Reapers could warp in from the brinks of the galaxy to wipe out life, the Protheans had technology far past any other races before them, with communication beacons connecting every one of their colonies, but the Reapers had doomed the Protheans far before they were able to inform the other colonies of the invasion. The Reapers had indoctrinated certain Protheans to survey their progress as a species, and to report to the Reapers on when the invasion should occur. The Reapers were able to take the Protheans by surprise, shutting off every Mass Relay linking the Prothean colonies, effectively blocking communications between the colonies. This inevitably makes the Protheans a centerpiece in Mass Effect's plot.
When the indoctrinated had revealed the locations of the last known colonies of Protheans, they were killed. Only one planet of living Protheans was left. At their last safe haven, on the planet Ilos, the Protheans created the A.I. Vigil, and life support chambers. The Protheans had developed Mass Effect technology on Ilos, and a small Mass Relay linking the planet Ilos to the Citadel. Vigil was programmed to awaken the Protheans once the threat had passed, but also to be self-aware of it's own energy, selectively choosing to shut down certain life support chambers of less important Protheans to preserve power.
The Protheans who were eventually revived realized there were not enough of them to repopulate, so instead they used the Conduit to reach the Citadel and deactivate the keepers in the Citadel in hopes of preventing the next Reaper invasion.
Vigil was still active when Commander Shepard and his crew arrived on Ilos to stop Saren Arterius, and here Shepard was told about the fate of the Protheans and the Reaper invasion.
Mass Effect 3
In Mass Effect 3 Commander Shepard is given the chance to have a living Prothean join with him to fight the Reapers and help end their endless destructions of life every cycle. It was revealed that the Prothean, named Javik, to join Shepard was a hero of his time, much like Shepard and he was put into a stasis so he could wait until it was safe to help build a new Prothean Empire.