The Autobots and their leader, Optimus Prime, find the AllSpark and crash land on earth. While on earth, they meet the human Sari and fight the evil Decepticons.
Optimus Prime and the Autobots continue to fight off Megatron and the evil Decepticons. Eventually, the team assumes heroic roles in Detroit City.
The Autobots must save Detroit from Starscream, when he kidnaps Bumblebee, Fanzone and Isaac Sumdac for ransom to get the AllSpark
Optimus Prime and the Autobots set up base at an old auto-parts shop. Meanwhile, Megatron's head comes back online and takes control of several robots to attack the Autobots and reclaim the AllSpark.
After having his funding cut by Porter C. Powell after Cyrus "The Colossus" Rhodes goes berserk during a demonstration, Prometheus Black experiments with the fluid leaked by Bumblebee which results in Prometheus becoming Meltdown. With his new melting powers, he vows to eliminate Isaac Sumdac.
Megatron has just made himself known to Isaac Sumdac and tricks the inventor into thinking that he is an Autobot. He then helps him in reprogramming some robotic dinosaurs after Bulkhead accidentally destroys them at a robotic theme park. While Sumdac tries to rebuild them, Prowl teaches Bulkhead how to 'think and move'. Behind Isaac's back, Megatron upgrades these Dinobots Grimlock (a Tyrannosaurus), Snarl (a Triceratops) and Swoop (a Pteranodon) to become his new attack drones. But during their 'rampage', both Ratchet and Bumblebee try to use an electromagnetic attack to disable them. However, Sari's key gets pulled into the mix, which gives the Dinobots a small semblance of 'a spark'. Megatron tricks' them into attacking the Autobots, which forces the Cybertronian heroes to battle them. It is during this fight that Bulkhead proves to be exactly what the Autobots need to stop the Dinobots, his muscle more than a match for the Dinobots muscle. Sumdac thinks it would be better to dismantle the Dinobots, and Prime agrees, but Prowl, who senses a life force inside them, and Bulkhead take the Dinobots to an island in the middle of Lake Erie where they can exist peacefully.
Ratchet thinks back to the time when he served in the Cybertronian War as a field medic. During the fighting, he was sent to rescue an Intelligence agent named Arcee who was injured during the fighting. The intelligence codes she possesses could turn the war in the Decepticons favor. For that reason, Megatron sends the the bounty hunter-for-hire Lockdown, to capture her, snagging Ratchet in the process. Back in the present, Lockdown has resurfaced and uses Ratchet's EMP generator to capture Optimus Prime. Recruited by Blitzwing and Lugnut to locate the Autobots who destroyed Megatron, Lockdown is revealed to be just a bounty hunter who doesn't care about the Decepticon's cause and just does it for the 'upgrades' he can get. Ratchet also reveals that the EMP generator Lockdown stole from him, which he used to repair injuries, doesn't work on the one bot it was designed for, namely him! But Ratchet also despises Lockdown for turning a medical tool into a weapon, and forcing him to use the generator to wipe out Arcee's memory so that the Decepticons wouldn't get hold of her security codes. But as a result, she wiped out every other memory she ever had, even of Ratchet and herself. Lockdown is apparently destroyed when his ship crashes into a bridge and Ratchet reveals to Prime that his encounter with Lockdown and Arcee is one of the reasons he is the way he is.
To obtain Destronium to help rebuild his body, Megatron bails a fleet-footed thief named Nino Sexton out of jail and gives him Isaac Sumdac's experimental super-speed suit to obtain the Destronium for him. Since the Destronium is highly unstable it needs to be transported quickly from the research lab to Megatron directly. Megatron uses Sumdac's private bank account to make Sexton do the job. Having arrested Nino Sexton before, the Autobots are shocked to learn that he now has super speed powers, which makes Bumblebee upset that Nanosec, Sexton's new name, is faster than him. Even with a pair of experimental rocket boosters created by Sumdac, Bumblebee is unable to truly catch Nanosec. However, the Autobots make two startling discoveries: 1-Nanosec's new speed suit is making him age rapidly, and 2-their constant movements are destabilizing the Destronium which will cause it to explode and take out half of Detroit. The Autobots use their combined talents (Bulkhead's battering arm, Prowl's jump boosters and Bumlebee's rocket boosters) to launch Bumblebee into the upper atmosphere where he hurls the Destronium away before it explodes.
It's Halloween and Sari introduces the Autobots to Earth's costume-and-candy traditions. However, the entire affair brings up bad memories for Optimus, who is haunted by the ghosts of his past, specifically when he and his fellow bots, the cocky and arrogant Sentinel Prime and power-mimicking Elita One were looking for a crashed Decepticon ship loaded with energon cubes. When Sari takes Bumblebee and Bulkhead trick or treating, the spider-like Decepticon Blackarachnia shows up and targets Sari's key. She wants the key to get rid of her organic half that she got when she was on an organic planet infested with giant spiders. The spider's venom somehow mutated her Cybertronian systems, making her 'a freak'. After seeing how Sari's key can heal Autobots, she wants to use it to purge her organic half. However, her body can't survive without her organic half now and as a result of using the key, she nearly kills off all organic matter in the entire city (which includes herself and Sari). Optimus gets the key away from her and Blackarachnia escapes, alone once again.
Megatron creates Soundwave, a robot in the form of a toy robot for Isaac to give to Sari for her birthday. Bulkhead is the only one who finds the toy to be a bad thing and finds out that the toy is evil. Unknown to Sari, the more she uses her key on Soundwave, the more he will evolve into a bigger robot.
When Megatron's two deadliest warriors, the split-personality Blitzwing and the strong, obsessively loyal Lugnut arrive on Earth looking for their leader Megatron, the pair tear up the city of Detroit. Optimus Prime and the Autobots battle the highly destructive Decepticons, only to get beaten back by their seemingly endless arsenal of weapons. Megatron, seeing that Lugnut is the most loyal, manages to make contact Lugnut and orders him to go an obtain Sari's key. With the key they can locate the Allspark and with that Megatron will be able to return to power. Optimus decides to use Sari's key to repair their ship so that they can get off the planet and lure the Decepticons away from them. But Sari doesn't want them to go and stubbornly refuses to help them, even to the point of sabotaging their ship. However, the Allspark reveals that if Megatron gets the Allspark, he will destroy everyone and everything in the universe. While Optimus and the Autobots battle Blitzwing and Lugnut, Ratchet and Sari reactive their ships weapons system and blast the pair into scrap.
When Sari gets kidnapped by the Dinobots, Prowl and Bulkhead go to the island to find out what is going on. Captain Fanzone goes after them, suspicious of their reactions to this situation. It is on the island that, after teaming up, the trio encounter the Dinobots, who attack them. Prowl is naturally confused at this, until he discovers that they all have acid burns on their bodies. Worse, it is the work of Prometheus Black (AKA the acid-shooting Meltdown) who has forced the Dinobots to become his watchdogs, and wants to use Sari as part of his experiments to create a transforming human. His previous experiments having failed, Meltdown thinks that a still-growing human, as opposed to an adult, will have better results, and chooses Sari because he hates Sumdac. Bulkhead is injured by Meltdown and Prowl and Fanzone team up to fight Meltdown's mutant freaks (the mammal-like one was his lawyer). They take out Meltdown by wrapping him in a non-corrosive containment suit and, after the Dinobots take out Meltdown's mutants, return to the city, leaving the Dinobots on their island.
Henry Masterson, creator of the Headmaster exo-suits, is fired by Isaac who states that Sumdac Systems doesn't make weapons of war even when it's exo-suit makes one of Isaac's robot models unstable. To take revenge on Isaac, Henry becomes Headmaster and plans his revenge by taking over Bulkhead's body. The Headmaster eventually succeeds in taking over Bulkhead's body, and fights the Autobots using it and weapons built into the Headmaster unit. He also causes the city's generator-core to overload, threatening to destroy the city. By the time the Autobots defeat Headmaster and knock the Headmaster unit off Bulkhead, the overload is at the point where the only way to stop it is to manually push the containment-grid back into position. However, nobody can survive the conditions inside the core, so it's essentially a suicide mission. At first, Optimus plans to do it himself, but Bulkhead has the idea of creating a new robot to do it. The Autobots create a patchwork robot in time, and Sari animates it with her key. The robot succeeds, and its melted, damaged, inanimate remains are put on display.
While camping in the woods, Prowl, Bumblebee, and Sari end up discovering Cybertronian energy readings in the forest. It gets worse when they have a run-in with parasitic Space Barnacles, that have apparently taken over the Cybertronian body of their thought-to-have-been deceased enemy Megatron, and end up taking over Prowl and Bumblebee. Sari uses hot water to destroy the space barnacles, but Isaac Sumdac finds the body and takes it back to his lab to rebuild it.
When Starscream, Blitzwing, and Lugnut begin their invasion upon Earth, Optimus Prime demands that Sari hand over her key. This causes her to run away only for her to end up captured by Dark Black Arachnia. Optimus begins to doubt his leadership when Megatron begins his next stage to have his body rebuilt.
Now that Megatron's body is rebuilt and designed to blend in on Earth, Optimus Prime, Prowl, and Bulkhead battle valiantly against him only to get brutally beaten. Then after punching Starscream, Megatron uses Sari's key to lead Lugnut and Blitzwing to Dinobot Island, unaware that Blackarachnia has beaten them to it.
Optimus Prime and his band of Autobots are taken off the job when the Cybertron Elite Guard, led by Ultra Magnus, comes to Earth looking for the AllSpark.
Optimus teams up with Sentinel Prime in order to defeat the Headmaster.
Unaware of the Decepticon activity, the Elite Guard take Optimus Prime and the Autobots back to Cybertron.
The AllSpark creates a new Autobot out of pieces of garbage.
Bumblebee competes against the Decepticons in an underground racing competition.
When the AllSpark turns construction vehicles into Autobots, Bulkhead becomes fast friends. However, the Decepticons have other plans in mind.
Prowl and a mysterious Decepticon bounty hunter go after Starscream.
The second-rate villains of Detroit team up to beat the Autobots.
While chasing an Autobot traitor, Bumblebee thinks back on the time he spent with Bulkhead in the Autobot Boot Camp.
Unlikely matchups! It's Optimus Prime and Dinobot Grimlock vs. Blackarachnia and Meltdown.
Sari has to defend the Autobot home base from invading Constructicons.
Megatron captures Bulkhead in order to take over Cybertron.
The Final Battle! It's Optimus Prime and the Autobots against Megatron and the Decepticons in a fate to save both Earth and Cybertron.
As Sari and Professor Sumdac deal with the fallout of the shocking discovery, the Autobots try to contact Cybertron to warn them of the traitor Longarm in their midst. Meanwhile, Megatron inadvertently stumbles upon a new plan to conquer Cybertron, where an increasingly desperate Longarm & Shockwave tries to cover his tracks.
In the aftermath of the battle at the mine, Sari and her father’s relationship takes a strange turn; the Autobots have their work cut out for them trying to contact Cybertron; and Megatron and Starscream find a new opportunity.
As Sari and Professor Sumdac deal with the fallout of the shocking discovery, the Autobots try to contact Cybertron to warn them of the traitor Longarm in their midst. Meanwhile, Megatron inadvertently stumbles upon a new plan to conquer Cybertron, where an increasingly desperate Longarm/Shockwave tries to cover his tracks.
Bulkhead and Isaac Sumdac try to rebuild the Space Bridge that Megatron had built. When Bulkhead convinces the Constructicons to help out, a combination of a forklift, a Headmaster unit and an Allspark fragment gives birth to Dirt Boss. Meanwhile, the others track down any remaining Decepticons and run into Lugnut.
A crazed Wasp finds his way to Earth to exact his revenge on Bumblebee... but he doesn't count on the Elite Guard following him.
Sentinel Prime has incredible success capturing fugitive Decepticons, leading Prowl to suspect he's getting help.
The Autobots and the Elite Guard pursue Wasp for their own agenda. However, Blackarachnia has Swoop capture Wasp in her latest attempt to rid herself of her organic half. This experiment goes awry and turns Wasp into Waspinator.
On Christmas Eve, Optimus Prime patrols the city in search of Soundwave. With Porter C. Powell selling Soundwave action figures, Optimus is paranoid that the real Soundwave is out there. When the Autobots drift off to sleep, they awake as full fledged humans. Now they must figure out what happened to them while dealing with a Decepticon onslaught.
It turns out that Soundwave has trapped the Autobots in a virtual reality intending to brainwashing them to his way of thinking. Now, Sari must free them before Soundwave completely turns them into Decepticons. She ends up gaining unlikely allies in Snarl, Scrapper, and Wreck-Gar.
The Space Bridge on Earth is finished. Meanwhile, the Elite Guard ship holding most of the Decepticon prisoners heads straight into an ominous space storm. The space storm reactivates Swindle who frees the Decepticon prisoners and takes over the ship. Optimus Prime identifies the "Broken Lance" code from Sentinel Prime and uses the Space Bridge to transwarp to the ship.
Ratchet activates Bulkhead's Space Bridge, which ends up sucking Captain Fanzone into it with Ratchet following him. They both end up on Cybertron around the time Sentinel Prime has declared a lockdown. Omega Supreme has arrived on Cybertron with Megatron, Starscream's head, and Lugnut. Thus, Shockwave (still possessing Ultra Magnus' hammer) attempts to get Omega Supreme's access codes from Arcee herself instead of Ratchet to reprogram Omega Supreme. In the end, Ratchet caught Ultra Magnus' hammer, Jazz joins Optimus Prime's team, and Arcee was shown to have her memory back.
The Autobots race to find an advantage over Megatron's control of Omega Supreme.
The Autobots fight to defend Detroit from Megatron and his clones of Omega Supreme.
