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.

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

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.

Both Autobots and Decepticons are facing tough times as they are in need of the element called Cybertonium. The Decepticons quickly get as much as they need, but the only way for the Autobots to get it is to rely on the Dinobots, who have been unaffected by all this. However, the Dinobots have been getting annoyed with the Autobots lately and leave them.

Failing to topple Megatron, an exiled Starscream plans his revenge. He uses World War II era machines and five personality components to create the Combaticons, which prove very powerful in their Bruticus form.

Elita-1, leader of a group of female Autobots causing trouble for the Decepticons, is captured and used as bait to lure Optimus Prime into a deadly trap. However, Elita-1's strange time manipulation technique saves him, but leaves her close to death. Her only chance for survival lies in Alpha Trion.

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.

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.

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.

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 trick Grapple and Hoist with claims of having left Megatron. They construct a tower Grapple thought up to absorb solar energy, which Optimus Prime did not want to be built for fear of The Decepticons getting their hands on it. Not surprisingly, The Constructicons betray them.

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.

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.

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

Megatron and a politician team up to slander the image of the Autobots.

Wheeljack's new invention, the Immobilizer, is capable of rendering any Transformer hit immobile for a short time. Once the Decepticons get their hands on it, however, they modify it and begin leaving many Autobots immobile.

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.

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

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 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.

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.

Both Autobots and Decepticons are facing tough times as they are in need of the element called Cybertonium. The Decepticons quickly get as much as they need, but the only way for the Autobots to get it is to rely on The Dinobots, who have been unaffected by all this. However, the Dinobots have been getting annoyed with The Autobots lately and leave them.

While Megatron and Shawn Berger enjoy Decepticon Day in Central City, Spike tries to find video evidence that proves the Autobots are innocent!

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 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.

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.

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.

The latest Decepticon plot to destroy the Autobots involves the creation of a Optimus Prime duplicate. They hope this duplicate will be able to convince the other Autobots he is the genuine article and will lead them into a chasm that will destroy them.

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.

Hoist gets a big break into show business after rescuing stuntmen. Sunstreaker, Powerglide, Warpath and Tracks are along for the ride as well. On the road to a movie career, however, they learn Dirge has stolen a device from Wheeljack's lab.

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

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.

The Junkions fall victim to subliminal messages from the Quintessons, who are trying to get a journal off the Planet of Junk. This also causes the Junkions to attack Sky Lynx and Astrotrain, which brings the Autobots and Decepticons into the situation. Unfortunately, a screw up makes the Junkions send out the subliminal messages on their own, bringing about mass confusion and destruction.

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

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

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.

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.

After the Autobots interfere with one of his plans, Victor Drath gets help from Ol' Snake (none other than the notorious Cobra Commander) to create artificial human bodies. Rodimus, Springer, Ultra Magnus and Arcee get caught and placed in the artificial bodies. Seemingly human, they will have to find a way to reverse what was done to them and stop Drath from using their original bodies against Autobot City.

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.

An alien is discovered to have a powerful weapon that fires crystals, which are taken from a creature Kup knows of, Chaos. Galvatron plans to construct his own powerful weapon on Chaos' home and several Autobots race to prevent him from using it on Cybertron.

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

Daniel leaves a banquet being hosted by his parents. He and Grimlock end up discovering a Quintesson chamber and get stuck in a magical world.

A hunter sets his sights on Optimus Prime and uses several captured Autobots to force him into a confrontation.

Astrotrain and Blitzwing leave The Decepticons to do things their way, which includes capturing Megatron and Starscream and seizing control of a stadium.

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.

The Decepticons attack a planet home to several Autobots and easily win as these Autobots prefer peace to fighting. Once the Autobots arrive, they try to persuade their peaceful comrades that only battling the Decepticons will solve their problems.

Astrotrain tricks a race living on one of Saturn's moons, Titan, into thinking he is a god and gets them to do his bidding, which includes getting a hold of a newly discovered power.

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.

Metroplex's transformation cog is taken by Swindle and First Aid blames himself for not stopping him. Meanwhile, Galvatron threatens to use a powerful weapon.

Megatron causes his fellow Decepticons to be infected with the deadly Cosmic Rust. Perceptor is captured to find a cure and he does, learning that element X will do the job. The Decepticons are cured, but then they use Perceptor to spread the Cosmic Rust to the Autobots and element X is in short supply.

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.

With the others rendered powerless, Smokescreen has to enter the gambling world to get the Energon needed to revive them.

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.

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.

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.

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.