Skywarp attacked him, but before Skywarp could report to Megatron, Jetfire shot him in the back, critically wounding him as he flew away. When Skywarp and Jetfire tracked Impactor's comm to Autobot Command, Skywarp was prepared to slaughter them all, but Jetfire took a stand and said wholesale annihilation for the sake of peace was wrong. Megatron advised Jetfire to 'take the shot' whenever the opportunity presents itself. Megatron was correct, and Jetfire subdued Magnus quickly. Later, when Ultra Magnus escaped torture and threatened to shoot Megatron in the back, Jetfire witnessed Megatron calling his bluff, believing he would never do something so dishonorable as fire at someone's back. After ordering the Seekers to go on patrol, he was put off by Megatron's description of soldiers as 'tools that can easily be replaced', and was appalled soon after when Megatron threatened to fire at Shockwave at close range. When Starscream rallied Decepticons to denounce Megatron and the plan to reformat the Autobots, Jetfire berated him for his false sense of superiority, leading to another scuffle that Megatron had to break up. When Shockwave presented his plan to reformat the Autobots into Decepticons, Jetfire noted to himself that it would be a victory without honor. Megatron ordered Jetfire to lock Ultra Magnus away in a cell when he failed to denounce the Autobots' role in the ongoing war. Megatron had to frequently silence their bickering. He later threatened to 'disarm' Starscream again. This earned the ire of Starscream and the other Seekers, and Jetfire briefly battled his own team instead of the enemy.

When Starscream threatened to attack them without his command, Jetfire sliced his hand off at the wrist with his arm-blade. Jetfire and his Seekers discovered Bumblebee and Wheeljack investigating a spacebridge.

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