After a vicious battle with the Decepticons, Spike is seriously injured. The Autobots use Sparkplug's new invention, Autobot X, as a body for Spikes mind until his human body can recover. But the side effects could be disastrous.
The Dinobots are destroying the Autobot base because there is no room for them to train. Bumblebee and Powerglide find a mysterious prehistoric island and believe it will be the perfect home for the Dinobots.
The Decepticons steal the Electro Cells from the research center and plan to use them to create energon cubes. When Mirage tries to stop them on his own, Cliffjumper begins to think that Mirage is a Decepticon spy.
The Decepticons set up a trap for the Autobots and kidnap Gears. Now, with Gears as his slave, Megatron creates a solar needle in order to steal the sun's energy. But the consequences could be disastrous.
When Autobots and Decepticons both begin to suffer from violent mechanical breakdowns, the cure for the condition is discovered on Cybertron. The Autobots' only hope for survival lies with the unaffected Dinobots. But Grimlock sees the crisis as an opportunity to rebel against Optimus Prime's leadership.
With the Dinobots captured by Shockwave, and the Autobots' malfunctioning reaching terminal levels, Spike and Carly must fight their way through the bowels of Cybertron to acquire the coveted Cybertonium element before all the Earth Transformers are rendered inoperable.
Omega Supreme used to be very different. He tells a story back when Autobots and Decepticons lived peacefully together. He remembers the friendship he had with the Constructicons. And the fateful day that changed everything.
Megatron wants to challenge the Autobots on the road, so he builds the Stunticons. But he needs Vector Sigma, the main computer on Cybertron to give them life. Now he must find the Key that will allow him to reactivate Vector Sigma.
Some Aerialbots start to have doubts about their cause, some have started to admire Megatron, and are thinking of switching sides. They get pulled into a time warp, and end up on Cybertron, before the current war began. They'll discover more about Megatron, and the origin of one of their own.
Megatron gets hit by some meteor fragments. The areas that were hit begin to rust. The Decepticons capture Perceptor to find a cure for their leader. But once cured, Megatron hatches a scheme to infect the Autobots with Cosmic Rust.