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.

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 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 Autobots and Decepticons find that the voices of three aliens (Allegra, Zebop Scandana and Basso Profundo) can make a powerful weapon.

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.

New allies for the Autobots are built, bringing about Grimlock, Slag and Sludge. However, the Dinobots prove hazardous to the Autobots and must be locked away. But they may be the only hope for the Autobots after a battle with the Decepticons.

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...

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.

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...

During a battle, the Protectobots finish off the Combaticons, with the exception of Swindle. Megatron orders Swindle to reconstruct his destroyed comrades or else a bomb in his head will go off, destroying him. As Swindle works to complete this task in time, three students get a hold of Brawl's personality component and use it for their science project, B.O.T., with disastrous results.

Daniel's nightmare troubles get a lot worse when the Quintessons make them real. Autobots and Predacons are forced to join forces in order to fight these nightmares.

Wheelie and Daniel want to have a party for Ultra Magnus after a recent good deed of his. However, Ultra Magnus' birthday is unknown, even to him. Wheelie and Daniel try to find out the answer from Autobot records. Unfortunately for them, Cyclonus decides to intervene.

A group of Autobots, Cyclonus and Quintessons become trapped within a Quadrant Lock Disc that has also kept the planet Zimojin and it's inhabitants trapped for thousands of years. To get out the Quintessons need a component belonging to Perceptor, but he has several parts taken out which are used by Katsudan to make repairs on a robot. Now in the small form, Perceptor learns the Zimojins were trapped there by the Quintessons out of fear.

The space bridge accidentally sends several Autobots and Decepticons to a strange world in which they are no bigger than toys.

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

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.

Marissa Fairborne and the Technobots encounter Dirk Mannis, who possesses the dangerous Recreator. Turns out the Quintessons want the Recreator for themselves and Dirk is happy to give it to them so long as he gets paid. Marissa and the Technobots get tangled into the resulting betrayals and scheming.

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.

Two planets are locked in a destructive war and the Autobots attempt to bring about peace. Things do not go so well, however, until a Quintesson Journal is found and provides evidence of Quintesson involvement in the war.

Spike is severely hurt during a battle. His mind is placed into Sparkplug's recent creation, Autobot X, until his body can be saved by an operation. But the Autobot X body was unstable to begin with and Spike soon ends up betraying his friends.