In his quest he captured the Autobots Nightbeat, Siren, and Hosehead, and extracted information from them. Then he saved a whale, to the other Decepticons' disapproval, because it could help lead him to the Matrix, which it did. When the Pretenders Jazz, Grimlock, and Bumblebee encountered him on the moon VsQs, he defeated them. Lord Thunderwing was always present in his Pretender shell, perhaps because he had mastered its strengths. He used the his knowledge of Pretenders' general weaknesses against Bumblebee by blasting his shell (knowing that Bumblebee would feel it even more) and nearly fried his circuits. Once again, he spared a life in the Decepticons' interests when he didn't kill Jazz, so that he could use his headlights to spot a creature in the shadows. This creature (revived by the Matrix's desire to experience evil) led Thunderwing to his prize.
By possessing the Matrix, Thunderwing's power was greatly augmented and he was able to combat Prime, and the Autobots aboard the Ark in space; but it was soon clear that the Matrix had possessed him when he fired upon one of his own loyal troops. Prime tried to save him when he realized he was a victim of the Matrix. When that didn't work, the Autobots shot Thunderwing into space harpooned to a shuttlecraft, which blew up.
During the Unicron war, Thunderwing's shattered body was seen on an asteroid with the Matrix above him. It revived him, and he flew to Cybertron in his space craft mode. This was the only appearance of Thunderwing transformed. Possessed, he attacked Unicron, but the tainted Matrix wasn't 'good' enough to finish the job. Unicron blasted them away and Thunderwing's last appearance showed his limbs breaking off as he was thrown through the Cybertronian air. [Note: His death was confirmed by the comic's producers.]