Jazz, Bumblebee and Sparkplug are up against insurmountable odds when Megatron manages to turn the recharging Autobots evil.

The Decepticon ship that shot down the Ark has been found and Megatron manages to find a component containing great power. With this power a danger to everyone, Perceptor, Bumblebee and Brawn shrink down and journey through Megatron's body to get it away from the Decepticon leader.

Megatron seizes control of the Torq III computer, enabling him to control the flow of oil.

After someone steals him, Tracks is briefly unable to transform or talk. This isn't so bad, however, as it leads to the discovery that Decepticons are planning to turn stolen cars into weapons.

Omega Supreme reveals his past to Optimus Prime, which involves a city's destruction, Megatron and Constructicons.

Innocent people fall under Megatron's control through music being played at a club.

The Decepticons are trying to learn the secret surrounding a man's invention and go after his teenage daughter. Powerglide intervenes to rescue her, but this causes her to fall in love with him.

The Decepticons acquire the Key that will give them access to Vector Sigma. After using Vector Sigma, they find the Key is also capable of making organics turn into machines. Megatron prepares to use it against Earth and The Autobots will need new allies in this battle, but their creation will come at a high price.

The Decepticons acquire the Key that will give them access to Vector Sigma. After using Vector Sigma, they find the Key is also capable of making organics turn into machines. Megatron prepares to use it against Earth and The Autobots will need new allies in this battle, but their creation will come at a high price.

Some Autobots take part in a charity race in Europe, but it's all a Decepticon ploy to obtain metal from Augie Canay's car in order to house the Pearl of Bahoudin. With their teammates damaged by the Stunticons, it will be up to Bumblebee, Bluestreak and Tracks to stop the Decepticon plot.

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.

A creature made out of energy, Kremzeek, gets made and causes trouble for the Autobots, Decepticons and Japan.

While much has changed and there has been a peaceful lull lately, the Decepticons are happy to get back to basics. Soon, Autobot City is a mess and the Plasma Energy Chamber key is stolen. The fight moves to Cybertron and in front of the soon activated the Plasma Energy Chamber, no less. An unexpected reaction from it, though, leaves a number of Transformers on both sides (plus Spike and Daniel) on Nebulos. Greater fighting awaits there, as machine-hating Nebulons seek to overthrow the evil Lord Zarak and the Hive. Getting back home is, of course, on hold for the recent arrivals to Nebulos. However, the Hive appears unstoppable and only something truly radical may work against them.

Daniel and four Nebulans join with five Autobots to battle the Hive, but the Hive decide to do something similar with a group of Decepticons. Meanwhile, Optimus Prime goes to Vector Sigma to find out the whereabouts of the missing Autobots and encounters an old face, learning the answer and what must be done.

After capturing Daniel and Arcee and acquiring the Plasma Energy Chamber key, Scorponok and the Decepticons make their way to Cybertron. The Autobots head after them, but Spike and Cerebros stay on Nebulos and come up with a strategy to use a Hive city as a weapon against Scorponok. Meanwhile, the Decepticons and Scorponok begin to threaten Earth and it is up to the Autobots and their allies to stop them.