The Rachni Wars were a series of conflicts beginning in approximately 1 CE (836 Before New Era), when an expedition from the Citadel Council activated a dormant mass relay . This relay opened a route to territory controlled by the rachni , a species of highly intelligent space-faring hive-minded insects. The rachni were alarmingly powerful, having massive strength in numbers, and extremely hostile. Negotiation with the rachni was impossible; their leaders, the rachni queens , dwelt in deep underground nests on worlds so hostile no one could survive them.
Discovering the Rachni
Around 1 CE (238 B.N.E.), Salarian explorers opened a mass relay to a previously-unknown system and encountered the Rachni, who promptly captured them. The Rachni used extensive research on element zero gathered from Kashshaptu to reverse-engineer the FTL drives of the explorers' starships. They proceeded to construct FTL vessels of their own and rapidly expanded into the galaxy, ushering in the Rachni Wars.
Attempts by the Citadel races to negotiate were futile, as it was impossible to make contact with the hive queens that guided the race from beneath the inhospitable surface of their homeworld. It was assumed that the Rachni were irredeemably hostile and could only be stopped through warfare, but the rachni had the upper hand and overwhelmed defenses with their sheer numbers.
Uplifting the Krogan
This period saw the Citadel races fight a losing war against the Rachni for nearly a century until the salarians "culturally uplifted" a new species, the Krogan . The volatile krogan homeworld, Tuchanka , had been ravaged by a nuclear winter caused by a krogan civil war. The Salarians helped the Krogan by giving them advanced technology and relocating them to a planet not cursed with lethal levels of radiation, toxins or deadly predators.
The true purpose of this salarian altruism soon emerged; the krogan were needed in the Rachni Wars as reinforcements. Unlike most Citadel species, the krogan had an extremely rapid breeding cycle. They had not only the numbers to drive the advancing rachni back, but the ability to endure the harsh conditions of the rachni planets.
The Krogan were able to strike at the queens in their lairs and quickly reclaim conquered Council worlds. When krogan fleets pushed the rachni back to their homeworld Suen , the rachni refused to surrender. The Krogan response was swift and brutal: they bombarded Suen's cities and detonated powerful bombs in the rachni's underground nests, obliterating them and creating massive sinkholes on the planet's surface. The Citadel Council would normally have objected to such total destruction, but after centuries of relentless war, complete eradication of the rachni seemed the only possible solution.
In 300 CE (537 B.N.E), the rachni were declared extinct, although in caution the Citadel Council left a listening post in the rachni's home system to monitor for any survivors. As a result of the Rachni Wars, the Council established new policies prohibiting the activation of any dormant mass relays that led to uncharted systems in order to prevent other disastrous encounters with undiscovered hostile races.
It is postulated that another party, possibly the Reapers , manipulated the rachni into starting the Rachni Wars. When confronting the Rachni Queen on Noveria , she will explain to The Shepards that she was unaware of why the rachni went to war against the galaxy. While in her egg, the Queen heard only the sounds of "oily shadows" and a "tone that hushed one voice after another" and "forced the singers to resonate with its own sour, yellow note." The Shepards allowed the Queen to live and escape from the Peak 15 facility, an asari acting in service to the rachni can be found on Illium who says that the Rachni are not an inherently hostile race. Shepard can question her on what might have caused the Rachni to attack upon their discovery by the Citadel races, and Shepard can suggest mind control. The Asari is uncertain, but the Rachni Queen's description of how her race was forced to resonate with a "sour note" is reminiscent of Reaper indoctrination .
Dr. Garret Bryson speculated that the mythical Leviathan was responsible instead, and may have been trying to create an army to confront the Reapers. Since the Reapers were in dark space at the time of the Rachni Wars and the ancient rachni bore no traces of the cybernetic augmentation that the Reapers utilize to convert organics into troops , Bryson believed that they could not have been responsible. Bryson attempted to use the activity patterns of the ancient rachni to track possible Leviathan artifact sites, but this parameter turned out to be irrelevant to the search and Bryson's theory remains unconfirmed.
Another theory has been made that the Combines could have manipulated the Rachni into fighting the galaxy to make it easier for them to conqure the said galaxy, though, few believe it to be possible but yet proven.