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On present-day Earth, the Decepticons were draining heat energy from the Earth's core by tapping in through the ice at the north pole, causing Earth to slowly freeze. Rumble was digging a tunnel with great trouble, when Skywarp started to mock him Rumble hit the ice with his piledrivers and caused a small cave-in that uncovered Skyfire. The Decepticons managed to reactivate Skyfire and bring him into Decepticon ranks, where he was put on guard duty.
When the Autobots arrived, he started to attack. During the fight, Sparkplug and Spike became stranded on an ice float, but were saved by Skyfire. He took the two to Megatron, whom he believed would not harm the humans. Megatron took them as prisoners, and Skyfire started to question his allegiance.
Later, as the Autobots searched the tunnels for Spike and Sparkplug, Ratchet, Ironhide, Hound, and Gears were seperated from the others and caught by the Decepticons. Skyfire was ordered to terminate them by Starscream. When Skyfire refused, Starscream shot him and seemingly destroyed the Autobots. In reality, he was tricked by one of Hound's holograms. Ratchet repaired Skyfire the best he could when the Decepticons attacked. During the battle Megatron and Optimus Prime were in a heated fight when Megatron saw that Skyfire was behind Optimus. Megatron then ordered Skyfire to destroy Optimus Prime. Skyfire then declared himself an Autobot and defeated Megatron and Reflector. Then, after a dog fight with Starscream, he destroyed the core-draining site and crashed, buried under the ice and snow.
Latter while the Decepticons were in Brazil seeking the Crystal of Power, Sideswipe and Wheeljack returned to the arctic to free Skyfire from his icy prison. Skyfire, Brawn and Windcharger then went to Brazil to check things out. Alone, Skyfire went to an Aztec temple where the crystal was kept, but had to return to save Brawn and Windcharger, who were in over their heads. They returned to HQ and picked up the rest of the Autobots and returned to Brazil. While the Autobots were battling Megatron and his warriors at a steel factory, Skyfire returned to the temple where he found an angry Thundercracker. Believing that he should let Skyfire destroy the crystal so Starscream would get in trouble, Thundercracker made no attempt to stop him. Starscream overheard this and tried to shoot Thundercracker. Skyfire got hit instead and was deactivated and left inside the temple. Bumblebee, Spike and a female native then found Skyfire, whom Spike repaired just in time to stop Ravage. He then flew outside the temple were the Autobots were fighting the Decepticons and their new weapon, powered by the Crystal. Skyfire destroyed the weapon while Ironhide had Megatron distracted. The Decepticons retreated, and the Autobots stopped the power flow that was left after the Crystal's destruction.
Later, Skyfire was seen when the Decepticons had used a super-space bridge to bring Cybertron into Earth's orbit. He was present again when the Autobots evacuated the base when the volcano became active again, and managed to save Huffer, Ratchet and Windcharger. He also went to Cybertron with Spike, Wheeljack, Trailbreaker, Bumblebee, and Brawn to rescue Sparkplug and cure him of his hypno-chip. Skyfire then flew the Autobots to an island where their friends were losing a battle against Megatron. Skyfire arrived in time to reinforce the Autobots, and Wheeljack was able to cure the remaining hynotised humans.
