At the start of the Autobot campaign, NEST Pilot Sgt. Epps is reporting Decepticons in Shanghai, China. Upon the arrival of the Autobots, Major William Lennox informs them there are Decepticons in the perimeter that must not escape, and Ironhide is sent to fight them. Ironhide then battles and defeats Sideways. When Optimus Prime gets word that Ironhide is missing, Ratchet heads out to find him and get him to safety. After locating Ironhide, his power is recharged and another Decepticon battle ensues. After annihilating Decepticon troops, Optimus battles Demolishor. Upon his defeat Demolishor states: "The Fallen shall rise again."The Autobots then head to Burbank, California where a previously unknown fragment of the AllSpark has surfaced in possession of Mikaela Banes. When the Decepticons detect the fragment, Bumblebee is sent to protect Mikaela. Meanwhile the Autobots learn that a second Allspark fragment held by the Americans has been stolen. Soundwave learns of Megatron's location in the Laurentian Abyss and transmits it to the Decepticons. Breakaway is sent to defend the carrier fleet Deep-6 which guards Megatron's corpse from the Decepticons. Despite his efforts, Megatron is reactivated.
On the East Coast, Sam Witwicky is kidnapped by the Decepticon troops and is taken to an industrial park near his college. Ratchet manages to locate Sam in an abandoned foundry and sends Bumblebee the coordinates. Bumblebee rescues Sam and takes him to the extraction point, upon which Grindor attacks Bumblebee. Following Bumblebee's victory, Optimus decides to give the humans a Cybertronian weapon called the Axion Gun to help combat the growing Decepticon threat. He personally escorts the Axion Gun to NEST headquarters. After getting the convoy to their destination, the Autobots escort Sam to meet with former Agent Simmons. With intel from Simmons, Sam has Bumblebee take him to the museum to seek out a robot named Jetfire. While Sam looks for Jetfire, Bumblebee defends the museum from the Decepticon troops. Jetfire emerges from the museum and takes Sam through the trans-dimensional Space Bridge to Cairo, Egypt; the Autobots then follow.
Jetfire reveals that the Dynasty of Primes have constructed a machine called the Sun Harvester hidden in an Egyptian pyramid. He says the device destroys stars to harvest their power, converting it into energon. Upon arrival in the outskirts of Cairo, the Autobots search for Sam while evading Decepticon troops. After locating Sam, Optimus Prime takes him to the Tomb of the Ancients. While Sam is in the tomb, Optimus and Jetfire defend it from Megatron and Starscream. Optimus defeats them, but they escape after Megatron impales Jetfire. The Fallen reveals himself and the Sun Harvester, powering its systems up and begging the harvesting of the Earth's sun. A dying Jetfire lends his wings and parts to Optimus in order to help Optimus defeat The Fallen. Elsewhere, Bumblebee ends up fighting and defeating Devastator. Optimus battles The Fallen, defeating him by impaling his face with his blade. The Fallen falls into the Sun Harvester and destroys it. With the Ancient Transformers avenged, Ratchet informs Optimus that Megatron escaped on a ship to a distant galaxy. Optimus then salutes his troops for their good work in stopping the Decepticons.
The Decepticon campaign begins in Shanghai with Sideways tracking down Autobots in his area. He then learns that Grindor has gone missing and that Sideways must find, repair, and transport Grindor to the extraction site. Once Grindor is safe, he attacks Autobots protecting NEST arrays and infects the arrays with a virus, giving the Decepticons access to NEST communications. Elsewhere, Long Haul destroys NEST bases located around Shanghai. Ironhide emerges to fight Long Haul but is defeated, and Starscream proclaims the victory as a warning to Optimus Prime.
The Decepticons then head to Burbank. There Soundwave has learned that Sam has given a shard of the Allspark to Mikaela. They formulate a plan to recover the shard and use it to revive Megatron. Long Haul captures men who may know Mikaela's location, who are then interrogated by Starscream. Starscream is able to discover Mikaela's location, and he sends Long Haul to retrieve her. Starscream receives word that the Decepticon troops transporting Mikaela have been intercepted by the Autobots. In the wake of defeat, the Decepticons learn of another shard held by American armed forces which is retrieved.
The Decepticons learn from NSA Chief Galloway that Megatron is buried deep in the Laurentian Abyss. Starscream disables the Deep-6 aircraft carriers that guard Megatron's remains in the Laurentian Abyss, allowing the Decepticons to gain access to Megatron's remains. Megatron is revived, and the Decepticons return to the east coast. Megatron disables Optimus Prime and has Starscream destroy a museum that Sam entered, but he is not among the ruins. They learn he was transported to Cairo, Egypt via a space bridge created by Jetfire. Megatron arrives on the outskirts of Cairo and engages Autobots in combat. Jetfire and Bumblebee challenge him, but are defeated. Elsewhere, Long Haul destroys the Axion Gun that the Autobots gave to the NEST Troops. Megatron learns that The Fallen has betrayed him by promising to make him a Prime, learning that Primes are born, not made. Megatron then destroys him before he can fully activate the Sun Harvester. Victorious, he begins plans to form an army of new Decepticons.
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