The Air Defense Team stop a satellite from falling onto Chicago, only to find that it was a bait for a trap by Starscream! The Decepticon sets about acquiring the three Mini-Cons, but is prevented when Optimus Prime, Hot Shot and Red Alert come along. Before taking flight, Starscream plants a tracker on one of the Mini-Cons.
Shockwave has taken over the leadership of the Decepticons and Megatron is his prisoner. The one-eyed freakazoid has taken up residence in the Ark and his first attempt at redecorating his new temporary home involves hanging up all the deactivated Autobots like slabs of beef.
The Air Defense Team prowl around a NASA facility looking for some deep space technology to help them get off Earth. Instead they run into an ambush, and get taken out by a human commando squad. They wake up in Area 54, Nevada, and discover that three Mini-Cons (the Land Military Team) were discovered by humans in the 1950s. The Air Defense Team escape, but decide that finding the Land Military Team will be their first priority.