After commander Shepard's famous "suicide mission" through the Omega 4 relay, The Illusive Man had his hands on what remained of the Collector Base and their project of creating a human-like Reaper.
Cerberus began to do a lot of experiments on the Collector in order to have a better understanding of their bio-technology, the way their hierarchy works, the way they share information, how their Seeker Swarms work and are able to disrupt armor systems. Few Collectors that were lightly damaged were transferred to Sanctum, in order to be re-animated and observed. Unfortunately for Cerberus, two of them became violent and managed to escape, inflicting heavy damage to the facility, causing problems with the organic-drone prototype. The security personnel of the installation then received an order to destroy those Collectors.