At first the reapers were considered a prothean legend but, commander sheperd continued to show that they were probably real however, the council denied these facts until they saw the reapers themselves. A reaper known as Soverign attacked the Citadel aided by geth fleets and troops. Commander Shepard's squad defeated the geth , Saren , and Soverign.
The Protheans and a number of other species were wiped out by the reapers. The Prorheans held for about a century and almost finished a weapon against them that the alliance later used. This weapon called " the crucible " gave Commander Shepard the option to either destroy or control the reapers.