The Decepticons have all retreated to the planet Char. They are leaderless and without energon, worst of all the moral is down to zero. Cyclonus decides to rescue Galvatron in order to restore the Decepticon army to its former splendor. Meanwhile the Quintessons finally decide to reclaim Cybertron, which they see as their possesion. After Galvatron is rescued, he assumes command of the Decepticons again. The Quintessons trick him in saying they can help him get the Decepticon Matrix (which doesn't exist) and so he forms an alliance with them.

The Autobots first think they were attacked by the Decepticons, but Rodimus Prime travels within the Matrix and there he learns the truth. Rodimus Prime visits Quintessa to free Ultra Magnus, Kup and Spike from the Quintesson. The Quintessons abandon Quintessa and push the destruct button for their own planet, only to destroy the Matrix which is still carried by Rodimus Prime. They fail, because Rodimus Prime and all the other Autobots on Quintessa are saved in time. The Quintessons are now without any planet of their own and are forced to travel from planet to planet.

The Decepticons and Quintessons plan their attack on the Autobots. On Earth the Constructicons create a gigantic Decepticon: Trypticon. The plan is that Trypticon will attack Metroplex on Earth and that at the same time the other Decepticons will launch an assault on Cybertron. Metroplex manages to defeat Trypticon. During the battle on Cybertron some Sharkticons try to activate a device to disable all Transformer. This plan of Quintessons fails because Spike is also on Cybertron and he isn't affected by the device. Galvatron wants to continue the battle, but Blitzwing orders Galvatron to stop the fight. Galvatron listens to Blitzwing, but he warns him that he will never be welcome in the Decepticon ranks again.

The Quintessons try a new plan to defeat the Autobots. They enter the tombs of the death Autobots and make some sort of zombie of Optimus Primes . Optimus Primes travels back to the Autobots and Rodimus Prime gives the command and the Matrix back to Optimus Primes and he becomes Hot Rod again. Optimus Primes then leads the Autobots into a trap of the Quintessons. Hot Rod sees through the Quintessons list just in time and he tries to stop Optimus Primes . Optimus Primes defeats Hot Rod in battle, but at the moment that he is about to kill Hot Rod, his old personality comes through. He gives Hot Rod the Matrix and then he takes the Autobot command ship into the trap, the trap is destroyed and the ship with Optimus Primes on board is destroyed.

A Quintesson scientist developed some sort of time window. He uses it to capture time energy. Perceptor notices the fluctuations in the time energy matrix of the universe and decides to investigate. Wreck-Gar, Blurr, Blaster, Ramhorn and Rewind go with him as an escort. They attack the Quintessons and by accident the Autobots that escorted Perceptor go through the time window and they arrive on Cybertron at the beginning of the rebellion (see earlier). From the past A-3 also comes through the time window, for the third time in history he plays an important role in the life of the Aerialbots. The Autobots drive off the Quintessons and return A-3 to his time and manage to get the other Autobots back from the past. Then they close and detroy the time-window.

A lot of events that are related to the past take place in the story. Grimlock and Daniel find on Cybertron a device used to exile Quintessons, the Quintessons used this device themselve when they were still masters of Cybertron. A planet is discovered inhabited by Transfomers that have fled from Cybertron at the start of the war between Decepticons and Autobots. This planet is destroyed, but all inhabitans are saved, including Sandstorm. Wheelie and Daniel find an astroid that was launched at the start of the war. The astroid contains files that the Autobots wanted to protect from the Decepticons. The Autobots are one time attacked by one creature that was locked up deep inside Cybertron. This was one of the creatures (partially robot, partially organic) that the Quintessons made before they started to make robots.

Octane is in exile from the Decepticons and has found sanctuary on Cybertron (apparently the scenario writers have confused him with Blitzwing). He is attacked and he flees to the lower levels of Cybertron, there in the halls of the Decepticons he encounters Starscreams ghost. Starscream is able to go from body to body and he can take control of that body. First Starscream takes Cyclonus body and tries to take control of the Decepticons, when that fails he tries to make a deal with Unicron. Starscream offers to repair Unicron if Unicron promises to give Starscream his own body again. The Autobots and even some Decepticons prevent Starscream from repairing Unicron and Starscreams ghost disappears into outer space.

Grimlock gets suddenly very intelligent after he bites some electrical circuits. During a battle he sees that the Autobots need reinforcements against the Terrorcons and quickly he creates the Technobots. The gestalt of the Terrorcons; Abominus, scares the Technobots and they ask Grimlocks advice. He explains that they have their own gestalt; Computron and then he transfers his newly received intelligence to Computron. Grimlock is his old stupid self again and Computron manages to defeat Abominus. Being stupid has its advantages as it is soon demonstrated.

Primacron has learned of his mistakes that he made when he created Unicron. This time he creates a creature of pure energy; Tornatron. The assistent of Primacron gathers all primitive thinking Transfomers, he reasons that since Tornatron can't be defeated by the most intelligent plans, so perhaps a stupid plan can work. All the primitives from Autobots and Decepticons are gathered on a planet, but Tornatron defeats them all. Grimlock escapes his attention and Grimlock is able to activate the reverse switch and defeat Tornatron.

Two humans rescue the body of Optimus Primes from the remains of the shuttle that he was in. They also discover a spore that brings hateness. One of the humans has a grudge against the Autobots and uses the spores against them. Rodimus Prime escapes the first contamination and rescues Optimus Primes s body. The spores are spreading through the galaxy and no one seems safe for them. A Quintesson agrees to restore Optimus Primes , because both he and Rodimus Prime think that Optimus Primes will be able to stop the plague. When Optimus Primes is restored he uses the powers of the Matrix to cure everyone. The Matrix has become an empty shell and Rodimus Prime is just Hot Rod again. The Autobots have finally Optimus Primes back in command.

Galvatron steals a key from the Autobots to open the plasma energy chamber on Cybertron. Hot Rod and some other Transformers get it back from Galvatron, but they get stranded on Nebulos. A group of Decepticons go after them and capture some Autobots. The remaining Autobots make a deal with the Nebulons and they become Headmasters. With this advantage they free the other Autobots. Now the Decepticons make a deal with the Hive and become Headmasters and Targetmasters. The Decepticons get the key from the Autobots once again. The Autobots copy the Targetmaster technology and become Targetmasters themselve. Meanwhile Optimus Primes uses the shell of the Matrix to enter Vector Sigma and he consults with Alpha Trion.

Lord Zarak from the hive makes a gigantic Headmasters: Scorponok. He takes the Decepticons and the key back to Cybertron. Spike makes a gigantic Headmasters Autobot: Fortress Maximus. Fortress Maximus defeats Scorponok on Cybertron, but after that Galvatron opened the plasma energy chamber. The energy starts to overload all Autobots and the sun. Spike suddenly sees a solution: he transfers all energy to Vector Sigma. Then an incredible thing happens: the Golden Age is restored. All Autobots are restored and they celebrate their victory.

The Decepticons escape in Scorponok and Galvatron already starts to make new plans to dominate the universe. Lord Zarak subtlely makes clear that it isn't necessary Galvatron that will be the leader of the universe.