Four million years ago, the "Arc" and Nemesis crash-land on Earth, and the Autobots and Decepticons go into stasis.
In the present day, Bumblebee awakens on Earth. He is briefly instructed by Ratchet about what has happened so far. A volcanic eruption awoke the Decepticons, who escaped. However, aside from the two of them, the Autobots are still in stasis, and need energon to be powered up. Bumblebee then encounters Frenzy. After dispatching the Decepticon, he meets up with Ratchet, who further explains what has transpired. They then encounter Soundwave, who is in the process of harnessing a human power plant to produce energon, and defeat him.
With the energon they've harvested from the power plant, the pair reactivates Metroplex and Optimus Prime before moving out to locate more power plants in their quest for energon to help energize their comrades. They eventually encounter the Seekers and Jetfire, whom they promptly defeat. Immediately afterwards, Prime convinces Jetfire to defect to the Autobot cause before sending him on a scouting mission. During this mission, Jetfire comes upon both Trypticon and Megatron. Megatron immediately attacks the traitor, but thanks to Jetfire's superior speed, he is able to escape and complete his mission of powering down three force fields that are protecting a space bridge. This is part of Prime's plan to return to Cybertron and rescue any Autobots still there.
The Autobots are able to break through to the space bridge and teleport back to Cybertron but discover this was all a trap by Megatron, who informs them that Shockwave had already captured all of Cybertron during their hibernation on Earth. The Autobots all rounded up, have their weapons taken, and are sent into the prison-cells. Ratchet and Bumblebee are able to escape and locate an armory in which to arm themselves before they free the rest of the Autobots, who then proceed to escape back to Earth to regroup.
When they return, they encounter the Decepticon Seekers and Tapes attacking Grimlock, whom they rescue. After fighting off the Decepticons, Grimlock immediately runs off to find more 'Cons to munch and ends up taking down a group of them himself.
Meanwhile, the other Autobots receive a distress signal, only to discover that it's a trap. They are just able to escape and return to the Ark, but discover that the Decepticons have followed them and are planning on a last-ditch attempt to capture the ship. The 'Bots are able to fight them off, thus ending the war on Earth, before Prime announces that the best way to end this war is to make a surgical strike at the Decepticon Shockwave himself.
They re-enter the space-bridge, and teleport to Cybertron before deciding that they need to take down a power facility which powers the automated defenses on Shockwave's fortress. After this, a specialized squad is sent to penetrate the fortress's defenses, while Bumblebee and Prime directly confront Shockwave.
Prime tells Bumblebee to flee and help the other Autobots, but 'Bee chooses to stay and fight. However, even their combined might proves no match for Shockwave, who single-handedly defeats them both. Just when all hope is lost, Grimlock comes onto the scene and turns Shockwave into confetti between his teeth, effectively winning the battle.
Afterwards, Grimlock says that he wants more 'Cons to crush, to which Bee replies that he should pace himself or there won't be any left. Grimlock agrees with his assertion, while Prime sadly contemplates that Grimlock will most likely get his wish of crushing more Decepticons.
