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

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 Quintessons use Wreck-Gar, Cyclonus, Ultra Magnus and Marissa as research subjects, watching how they interact. Unfortunately for all of them, the ship they are on is heading for a black hole and this unusual group will have to work together to survive.

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 Quintessons plan to use a portal through time to prevent the Transformers' revolt against them. Several Autobots wind up getting sent back to the fight and a robot with an important future arrives in the present. And the Quintesson time portal begins to have disastrous effects on the universe.

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.

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.

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.

Galvatron goes into therapy, but it does not exactly agree with him. Every one of the doctors' attempts at treating him fail before they consider using one last option. Cyclonus tries to stop them, however, after learning it would make the Decepticon leader an invalid.

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.

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.

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.

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.

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.

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.

While much has changed and there has been a peaceful lull lately, the Decepticons are happy to get back to basics. Soon, Autobot City is a mess and the Plasma Energy Chamber key is stolen. The fight moves to Cybertron and in front of the soon activated the Plasma Energy Chamber, no less. An unexpected reaction from it, though, leaves a number of Transformers on both sides (plus Spike and Daniel) on Nebulos. Greater fighting awaits there, as machine-hating Nebulons seek to overthrow the evil Lord Zarak and the Hive. Getting back home is, of course, on hold for the recent arrivals to Nebulos. However, the Hive appears unstoppable and only something truly radical may work against them.

Daniel and four Nebulans join with five Autobots to battle the Hive, but the Hive decide to do something similar with a group of Decepticons. Meanwhile, Optimus Prime goes to Vector Sigma to find out the whereabouts of the missing Autobots and encounters an old face, learning the answer and what must be done.

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.

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.

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.

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.

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.