Just before Sovereign makes its shocking reveal, Shepard and company learn Saren's main base is situated on the planet Virmire, where he is conducting interesting experiments. The Krogan, bipedal reptilians from planet Tuchanka, were the victims of a terrible virus dubbed the Genophage. The Genophage drastically increased the probability of stillbirth in Krogan pregnancies, leaving them a dying race.
The Krogan have lived like this for hundreds of years, knowing they are a doomed race. When you get to Virmire, however, it is revealed that Saren has developed a cure. This is quite a shocking moment for anyone familiar with Mass Effect lore. Shepard must then decide to cure the Krogans or dispose of the cure before Saren can build his army.
