Sovereign is a gigantic starship of almost unimaginable power and sophistication. It was originally believed that the ship was a Reaper vessel that Saren Arterius found. But Sovereign is in fact an actual Reaper, a fully sentient and extremely powerful AI, which is why the geth obey its commands.
Sovereign is also able to control organic life through the process of indoctrination. A subtle field or signal surrounds the Reaper, gradually affecting the organic's mind until they are little more than a shell of their former self, bent on doing Sovereign's will. It has nothing but contempt for any lesser beings, seeing them as fleeting and temporary, whereas the Reapers are eternal.