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Arcee held the information needed to make Project Omega work but in order to keep that data away from Lockdown who was working for the Decepticons, Ratchet used his EMP generator to wipe her memories. Later, he worked with Ultra Magnus to try and recover the memories in the mind wiped Arcee through open processor surgery which accidently activated the failsafe retrieval program which transmitted the activation codes into Ratchet. Once the data was recieved, he was transfered to Project Omega to finish it. The Project's intention was to create a prototype Autobot weapon of mass destruction and give the Autobots the last chance of defeating the Decepticons.
Omega Supreme was a product of Project Omega.