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.
Proving to be a danger even to their own allies, the Dinobots are sent away to train on a recently discovered island in the hopes that they will learn how to effectively work together. The island, however, is far from ordinary as it is populated by dinosaurs. Meanwhile, the Decepticons make advances toward the island so they can acquire it's natural resources.
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.
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.
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.
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 Autobots capture the Stunticons during one of their thefts. With the Stunticons now imprisoned, Wheeljack presents a way to disguise Autobots as them. Going undercover, Optimus Prime, Jazz, Mirage, Sideswipe and Windcharger infiltrate the Decepticons and learn the Stunticons were trying to steal a part for a laser. However, the plan hits a snag after the real Stunticons escape.
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.
It is the year 2005. And the battle between the heroic Autobots led by Optimus Prime and the evil Decepticons led by Megatron. Two warring factions of transforming robots from the planet Cybertron. The Autobots must save their home planet from an evil entity known as Unicron, who's ready to consume anything that stands in its way. At the same time, they must defend themselves from an all-out attack from the Decepticons.
Beginning with a recap of the coming of the Transformers to Earth and the story of Devastator, the OVA then gets its original story underway, as the Autobots are shown to be in the midst of constructing the powerful "Scramble City," overseen by their newest arrival, Ultra Magnus. When the Decepticons learn of this, their combiner robots are deployed to attack, and a battle between them and their Autobot counterparts ensues.
While everyone continues to rejoice in their victory, unknown assailants capture Ultra Magnus, Kup and Spike. After being told by an 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.
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.
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.
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.
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 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.
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.
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.
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.
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.
The Decepticons get the Plasma Energy Chamber key after an attack on Autobot City. A group of Autobots manage to get the key back after Scourge opens the chamber, but it's energy accidentally sends them to Nebulos, a world locked in civil war between the evil Hive (controlled by Lord Zarak) and rebels that despise machines. The Decepticons pursue the Autobots there and they all get involved in the war.
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.
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 Secret Files of Teletraan II were a series of short (1–2 minute) profiles which aired in 1986, after select episodes of the third season of the original Sunbow cartoon series. They included recaps of past events, character and group profiles, and "where are they now" guides, helping to explain the 20-year time gap between seasons 2 and 3 to viewers who had not seen The Transformers: The Movie.