Optimus Prime is back and leads a team to Charr to retrieve the ship alloy from Galvatron. Galvatron guides them to it's location, but they confront a couple dangers and must fend off infected Transformers. Optimus and SkyLynx are the only ones not infected and barely get away with the alloy. The alloy is used to safeguard Optimus from the Hate Plague for his battle against Rodimus as the Matrix is the key to the cure.

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.

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.

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.

Galvatron learns what has been going on recently and meets up with the Quintessons. Rodimus again looks for answers, discovering the bitter history between Quintessons and Transformers. The Quintessons created the Transformers, but their creations rebelled against them. And the Quintessons are eager to exact revenge.

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

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.

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.

The Constructions use the newly created Trypticon to battle Metroplex, who is still unable to transform, on Earth. Sky Lynx tries to get the needed cog for Metroplex, which is with Blurr and Wheelie, but gets into a fight of his own. The Autobots and Decepticons continue fighting on Cybertron, until the Quintessons manage to immobilize them, leaving only Spike to save the day.

The evil Primacron plans to use an energy being named Tornadron to defeat the Transformers and help in his universal conquest. Meanwhile, the animal form Transformers leave during a battle between Autobots and Decepticons upon getting a strange signal. The signal was apparently sent by Primacron's own assistant, who believes this group of ""Primitives"" can defeat Primacron.

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.

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.

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.

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.

A meteor is about to crash in the earth and maybe be a good to get a lot of energy, so Optimus Prime order the Dinobots to guard the meteorite to avoid the Decepticons take this energy, but Megatron has a plan to use the Dinobots against Optimus Prime...

Starscream is going to destroy the Earth and take the energy from the explosion to rule the Universe. The Autobots and Decepticons must team up to stop that disaster.

The Earth is returning to the ice age, becuse an evil plan of the Decepticons who have found a new partner...

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.

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

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.

Grimlock becomes a genius after trying to stop anti-electrons (released by Scukzoid and Slizardo) from causing disruptions in the new power generator. This proves very useful to the Autobots, especially when Grimlock learns Unicron is the source of the anti-electrons. The Autobots journey to Unicron to prevent more anti-electrons from being obtained, but Galvatron and his forces are also heading that way.

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.