In issue #4, a human named Sparkplug Witwicky poisoned fuel used by both Autobots and Decepticons which caused both sides to fall in battle. At the conclusion of the battle, Shockwave arrived to finish off the Autobots.
Following Shockwave's destruction, Shockwave began to rebuild the decepticons while relegating Megatron to second in command.
Megatron, never one to accept being second in command, pretended to accept his new position while plotting to retake command of the Decepticons from Shockwave.
Unknown to Shockwave, the Autobot Ratchet survived the assault. Ratchet returns to the Ark to find that it is now controlled by the Decepticons. Ratchet, with the help of a human named Buster Witwicky, returns to the Ark. Inside the Ark, Buster finds the remains of the Autobots, including the severed head of Optimus Prime.