We sneak through the Mu Relay to stop Saren in his quest for the Conduit. After fighting his Geth we follow him into an ancient Prothean facility. Although the battles are juicy, the main purpose of this mission is for exposition. We encounter a VI, Vigil, who tells us much.
The Reapers spend their down time in Dark Space until a civilization is ripe. Then they activate a mass relay hidden in plain sight on the Citadel — it’s that silly statue that hums in the water feature — and enter the governing heart of the galaxy. From their they control everything and decimate at their leisure.
The Protheans, the species that was reaped last time around, were very close to breaking the cycle. Only a few scientists remained, the Protheans nearly extinct. They created their own mass relay, the Conduit. Before they died they transported into the Citadel and altered the Keepers’ programming. Those bugs at computers on the Citadel are actually responsible for sending a signal to the Reapers in Dark Space, awakening them and opening the portal. When the signal never happened, Sovereign came looking for the answer. Right now, the relay at the Citadel is locked down. But when Saren uses the Conduit he’ll reverse that signal and open the gate.
The Keepers, who now just do as the Citadel directs, were probably the first conquered species eons ago. They evolved, though, out from under Reaper control. The disdain for organic life and its evolution is a constant in any conversation with Sovereign. Now the Reapers have chosen to ally with the Geth, another machine race. Sovereign and the entire Geth fleet arrive at the Citadel space as Saren transports in and heads for the master control unit of the station.
Chasing him, we use the Conduit, too. The Citadel is a wreck, overrun with Geth, but we fight our way up the tower for a final confrontation.