Starscream is now in charge of the Decepticons, but all he does is lead them to defeat in battle against the Autobots. But things are about to get much worse when Megatron returns, setting his sights on a new and powerful anti-matter formula.

The Decepticons raid the Ark after tricking the Autobots with a distraction and Sparkplug gets captured. They use a device called a hypno-chip, created by a human named Dr. Arkeville, on Sparkplug to gain control over him. It is all apart of an evil plan to get a work force to create a new space bridge and bring Cybertron to Earth.

Natural disasters plague Earth as The Autobots attempt to stop Megatron's plan. A team of Autobots and Spike head for Cybertron to save Sparkplug, but they could be heading straight for a trap.

The Autobots on Cybertron evade capture and work toward finding a way to counteract the effects of the hypno-chips. Meanwhile, Optimus Prime leads the remaining Autobots in a battle to put an end to Megatron's plan.

The Autobots discovers that the Decepticons are trying to make a new weapon with the energy from the center of the Earth, controlled by a gem in a pyramid in Peru. The Autobots needs some backup from their old friend Skyfire.

The Decepticons discovers an old type of Decepticons, the Insecticons. They will ally to destroy the Autobots, who will have to face them in another great battle.

The legendary Atlantis is proven to be real and it's residents aren't exactly peaceful.

The Insecticons become extremely powerful after they consume an energy source. They enslave every Decepticon except for Megatron. The Decepticon leader and the Autobots will have to team up to return the Insecticons to normal.

The Decepticons plan to take New York and turn it into their new home base, disassembling Optimus Prime in the process. The rest of the Autobots must save Optimus and New York City without their leader.

Spike, Hoist and Warpath find their battle with a group of Decepticons interrupted when they all get sent back in time to the middle ages.

Seaspray falls in love, but the object of his affection is part of a rebel movement on another world.

The Decepticons work with a smuggler to take over a Mideast palace and begin acquiring plane parts for the construction of a air fortress. The Aerialbots head to the scene, but Slingshot and Sky Dive get into trouble. But a young man known as Hassan comes to their aid to help save the day.