After her defeat, Benezia reveals that Saren's flagship, Sovereign, isn't just a ship with mind-control capabilities. Sovereign is alive. Later, Shepard is confronted by Sovereign, who explains that all of the technology thought to be Prothean is actually Reaper technology. The Reapers allow organic life to develop for 50,000 years before they appear to harvest it.
The 50,000 years is almost here and Sovereign is making preparations for his sentient spaceship brethren. Mass Effect's shocking moments doesn't get much more shocking than this.
