Ratchet returns to the Ark and finds Optimus, who tells him to never give up hope. He then faces Megatron and makes an agreement: if he defeats Shockwave, then the Ark is his once more, but sure of Megatron's treachery, he sets out to find the Dinobots (buried in the savage land).
Josie Beller creates a special exosuit to wear to help overcome her injuries (paralysis) at Shockwave's hands in issue 6. She comes up with the name Circuit Breaker, and vows to destroy all robots, good and bad (Autobots and Decepticons), since they were responsible for her condition (even though it was Shockwave).
Shockwave creates the Constructicons to destroy the Autobots. The Constructicons then later merge into Devastator when faced vs. the Autobots' attack ,but are defeated. Shockwave then wonders why they failed if he supposedly received the creation matrix powers from Optimus Prime (since he doesn't know that Prime passed on the full effects to Buster).
Shockwave creates yet another robot to destroy the Autobots named Jetfire. However, Buster takes control of him using the creation matrix, and saves the Autobots from destruction, but is taken to Shockwave by Jetfire (unaware that he's still under Shcokwave's control).
Shockwave uses Optimus Prime's body (with a fake head created by Shockwave) to attack the revived and repaired Autobots. All seems lost, until the real Optimus's head appears and takes control of the fake head, thereby destroying it. The creation matrix is then returned to Prime by Buster,after Ratchet returns Prime's head back to his body.