A battle with the Decepticons leaves Optimus Prime damaged. Several Autobots journey to Cybertron to retrieve a vital part that will help repair him, but the Decepticons take advantage of the situation and launch an attack.

The Constructicons, recently created for the Decepticons, have built a device to give Megatron the powers and skills of his soldiers. All this is to give him the advantage in a challenge he issues to Optimus Prime. And if Optimus loses, he and the Autobots must leave Earth.

Octane is on the run from The Decepticons. He is forced to hide in a crypt, where the ghost of Starscream lies in wait and then takes over Cyclonus.

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 Decepticons have managed to construct a device that, once successfully tested, will allow them to travel to Cybertron. Later, they use a reprogrammed Bumblebee to make sure the Autobots walk into an ambush.

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 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.

Proving to be a danger even to their own allies, the Dinobots are sent away to train on a recently discovered island in the hopes that they will learn how to effectively work together. The island, however, is far from ordinary as it is populated by dinosaurs. Meanwhile, the Decepticons make advances toward the island so they can acquire it's natural resources.

The Decepticons' tampering on the island creates openings to other times, allowing all sorts of things from various times to arrive in the present. The Autobots race to reverse this before it's too late and to stop the Decepticon plot. But in the end, their best hope may be the Dinobots.

Failing to cause a divide between the Decepticons and Insecticons, Mirage's mind suddenly becomes enslaved and he is used by them in a plot against the Autobots.

The Decepticons send the recently stolen Nightbird on a mission to steal an informative chip from the Autobots.

The Decepticons plans to take energy from the center of the sun using a circuit from one of their enemies, Gears. The Autobots must defeat the Decepticons and rescue their compatriot.

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.

While everyone continues to rejoice in their victory, unknown assailants capture Ultra Magnus, Kup and Spike. After being told by a alien, a group of Autobots suspect the Decepticons are the culprits. But when they arrive at Charr, they find the Decepticons in no shape to pull off a kidnapping, meaning another is responsible.

The Autobots make it out of Charr, but Rodimus is down and looks out. In reality, he has made a trip to the Matrix and learns the Quintessons are behind the kidnapping. After Rodimus is revived, a rescue mission is soon underway. Also, Scourge and Cyclonus finally track down a battle hungry Galvatron.

The destruction of Quintessa causes the Autobots to arrive at Goo and poor Springer loses some parts. Blurr and Wheelie are stuck in a hostile place and are in need of some help. Meanwhile, the Quintessons agree to give vital energy to the Decepticons so long as the Autobots are destroyed.

On the run from Galvatron, Spike, Daniel and several Autobots enter a mausoleum and find a surprisingly not dead Optimus Prime. This would be cause for great excitement among Autobots. Unfortunately, however, Optimus is really under Quintesson control and is being used in a plan against his friends.

Starscream, in Scourge's body, attempts to complete three assignments for the damaged Unicron in exchange for getting a new body.

The Quintessons trick the Decepticons into releasing the dangerous Trans-Organics. One of them, the Dweller, begins taking control over Autobots and Decepticons alike.

Being the leader takes it toll on Rodimus and his attempt to relax gets him into a fight, in which he loses the Matrix. The Stunticons escape with it and Rodimus reverts to Hod Rod. At first, Hod Rod is perfectly fine with no longer being in charge, but he soon understands he must get the Matrix back. It will not be easy, though, as Scourge has already seized the power of the Matrix.

While testing a new ship alloy, Jessica Morgan and Gregory Swafford (who hates Transformers) stumbled upon the ship Optimus Prime was on and saved him. Some time afterward, Jessica gets hurt in a battle between Protectobots, Technobots and Terrorcons, causing her father and Gregory to plot revenge. They use Optimus to lure the Autobots into a trap, getting them infected with Hate Spores which make them go berserk. As the infection spreads, Sky Lynx seeks out a Quintesson that could bring Optimus back to life.

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.

Octane locates the defeated Trypticon and brings him to Carbombya. There, they follow orders from Fakhaddi in order to get energon. They begin stealing landmarks around the world for him.