Megatron captures Dr. Onishi, and the Autobots ally themselves with his son, Koji, vowing to safely recover him from Megatron’s clutches. An assortment of plans by Megatron to steal the Earth’s energy ensue, led by his subordinate, Sky-Byte, but are stopped by the Autobots, including the newly introduced teams, Team Bullet Train and the Spy Changers. Probing Doctor Onishi’s mind, Megatron discovers the significance of an ancient cave system, in which the Autobots discover a coded microchip belonging to the Doctor. After scuffles involving the new Autobot troops Skid-Z and Tow-Line, the microchip leads the Autobots to the Cave of the Dragon, where they discover a mysterious artifact of Cybertronian origin.
Further information decoded from Dr. Onishi’s microchip leads the Autobots to the site of a crashed Cybertronian spaceship containing six protoform Autobots. But Megatron has also learned of the ship through his mind-probes and attacks, capturing the Autobots and taking them to a nearby military base, where he scans vehicle modes for each of them and infuses them with his own Spark energy, creating the evil Decepticons. The final Autobot scans Optimus Prime in addition to the tanker truck that will be his alternate mode, creating Scourge, a twisted “evil twin” of Optimus. Several battles with the Decepticons ensue, as Sky-Byte grows steadily jealous of the attention Megatron heaps on his new warriors. Amidst battles between the Decepticons and the newly promoted Autobot subgroup, the Build Team, Sky-Byte attempts to prove his worth by holding a tower of humans hostage in exchange for the Autobots’ O-Parts, one of which is the artifact from the Cave of the Dragon. The plan meets with failure, but when Sky-Byte saves his hostages’ lives, Koji begins to think he might not be all bad. Subsequently, Ultra Magnus, the bitter brother of Optimus Prime, arrives on Earth to claim the Matrix in Prime’s possession, leading to an injured Optimus Prime facing certain doom against the Decepticons on a desert island. Magnus offers him the hand of friendship, but it is a ruse to allow Magnus to take the power of the Matrix, with an unexpected side-effect – the two brothers merge into Omega Prime and defeat their foes…
