The next two issues involves Ratchet sneaking into the Ark and confirming Buster's scouting report (Buster heads home with a bunch of college students he and Ratchet just happened to come across. He later get inklings of his new powers after a fight with Jessie and O. Thankfully, this was O's last appearance that I can recall.) Prime gives him a pep talk and tells him that he's taken steps to protect the Creation Matrix. (Pre-Furman it was a code that created new Transformer life, not a Matrix of Leadership knock-off.)
Ratchet tricks Megatron into allowing him to reactivate the Dinobots, but in the end Ratchet himself defeats Megatron (leading to #13) and reactivates the Autobots. If I had an account, I'd post those issue myself, but now you know the rest of the back-story. Good day.