The first issue follows the story of the film from Starscream's perspective, with him organizing his team to follow Megatron to Earth. During the battle in Mission City, Starscream is enraged by Megatron's uncaring attitude towards the death of his comrades. Following his leader's death, Starscream meets with a wounded Barricade (whom Ironhide caused to crash into a barrier and thus miss the battle) and is told the dead Frenzy had important files on Sam Witwicky and the All Spark. Starscream tells Barricade to carry on his role as his spy on Earth, while he flies to the Hoover Dam to recover Frenzy.
In the second issue, Starscream retrieves Frenzy but is injured, and he is forced to return to Mars in F-22 Raptor form. He explains to Thundercracker he likes his Earth form though, admitting he admires the humans for killing Megatron and destroying the All Spark. The two Seekers decide to return to Cybertron, using Frenzy's data to recreate the All Spark. They begin transmitting the data to Cybertron, and prepare to enter a Space Bridge. Starscream is confident with Optimus Prime on Earth, no one can stop his conquest of their home planet, unaware an Autobot team (consisting of Arcee, Cliffjumper, Air Raid, Camshaft, Smokescreen and Cosmos) are about to attack.
The third issue opens with the Autobots being engaged by a swarm of drones. They easily rip through them, even killing Hardtop, but are put on the defensive as Thundercracker arrives, killing several of them. Arcee, furious at history repeating itself as her colleagues fall, manages to badly wound him, but it is too late: a recharged Starscream arrives and kills all but her. The Decepticons return to Cybertron, with Ramjet having prepared things for his new lord. The data transmitted has been used, and a new All Spark is now under construction.
The series is consistent with Target Corporation's second prequel comic to the film with Wreckage being killed by humans upon arriving on Earth. However, the third issue refers to the torture of Bumblebee's squad (including Arcee) by Megatron, an event which took place in the first issue of the original prequel series, which seemingly takes place in a different continuity. The Transformers use spaceships, the absence of which in the film is explained by the Decepticons parking theirs (the Nemesis) on Mars before flying as protoforms to Earth