Sovereign was the first Reaper encountered by the modern Citadel races. Military leaders initially assumed that Sovereign was a geth or Prothean flagship commanded by Saren Arterius, a rogue Spectre. The truth was far more alarming. The massive ship was itself intelligent, and Saren proved to be under its control.
The attacks by Sovereign against Eden Prime and the Citadel removed any uncertainty about the Reapers' technological superiority. Sovereign's formidable shielding and firepower allowed it to hold off the combined fleets of the Citadel, and its mass effect fields proved powerful enough to let the enormous vessel land on a planet's surface.
Sovereign's mission -- to open a mass relay that would transport the other Reapers from dark space -- proved its undoing. During the Battle of the Citadel, Sovereign linked its consciousness to Saren's. When Saren's death corrupted the signal and shut down Sovereign's shields, Sovereign's destruction soon followed.