Sari Sumdac is coping with the newly discovered fact that she's a robot. Meanwhile, the Autobots on Earth are trying to figure out a way to warn the Autobots on Cybertron about the spy working for Megatron. Later, Megatron and Starscream find Omega Supreme and set a devastating plan in motion.
Things quickly descend from bad to worse for the Autobots when Detroit is menaced by new threats. Meanwhile, Ratchet remembers his first encounter with Omega Supreme and grows frustrated with his uselessness to the Autobots, all while Megatron and the Decepticons enact their plans.
Bulkhead must face off against the Constructicons and their new leader, Dirt Boss, when they decide to hold the city's oil supply hostage. Meanwhile, the other Autobots manage to capture Lugnut, but find hauling him away a more difficult task.
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.
In an effort to speed up their return to Cybertron, Sentinel Prime has Jazz pilot the Elite Guard ship through a space storm. The storm's energies reactivate Swindle, who frees his fellow Decepticon prisoners. Sentinel Prime sends a distress call to Optimus Prime, who uses the newly completed Space Bridge to TransWarp to the ship, where he helps fight back against the Decepticons.
A TransWarp accident with the Space Bridge sends Ratchet and Captain Fanzone to Cybertron, where Sentinel Prime has the planet on high alert. They soon end up stumbling upon a plot by Shockwave to steal Omega Supreme's Access Codes from Arcee.
The Autobots discover Omega Supreme's energy signal on the Moon. Rachet insists on going there right away to save him, but Prime refuses, knowing that they are too weak to fight Megatron. Ratchet, Sari and Professor Sumdac build flight boosters for Optimus to even the chances. Prowl tries to put the Allspark back together, using processor over matter.
In Part One, Megatron used Starscream's cloning technology together with Omega Supreme's activation code which Shockwave retrieved from Arcee to create clones of Omega Supreme which he could control through Lugnut. In Part Two, the Autobots must determine a way to defeat the powerful clones, and hopefully recover Arcee from capture at the same time.