Thundercracker was first seen during the Unicron Singularity crisis, as a loyal Decepticon serving Megatron and Starscream. Ordered to look for and attack whatever Autobots he could find, Thundercracker opened a warp gate to Earth. Before emerging, he scanned a nearby Sukhoi Su-35 jet for disguise, and liked it. Thundercracker soon spotted Landmine walking through a Colorado forest with three human children. He attempted to blitz the group with missiles, only to miss completely. He then found himself tangling with an airborne Optimus Prime, whose Super Mode proved impervious to missile fire. When Prime detonated Thundercracker's next missile volley in the Decepticon's own face, 'Cracker beat a hasty retreat via warp gate.
While Thundercracker worked for Megatron, he helped him find the Cyber Planet Keys and orbit the entire universe with them. He even worked with Starscream for a while, until Starscream betrayed Megatron and began craving Omega Lock and Cyber Planet Keys for himself. When Megatron found his way to the Gigantion and began looking for its Cyber Planet Key, Thundercracker explored one level that could lead to the Cyber Planet Key, and at the same time had to fight Jetfire.
When Galvatron stole the Omega Lock, he was going to use it and the Cyber Planet Keys to unleash the black hole, Thundercracker and the other Decepticons serving Megatron began fighting Optimus Prime and his friends. But Optimus Prime and Leader Transformers managed to defeat Galvatron, get the Cyber Planet Keys and the Omega Lock back, destroy the black hole, and save the universe. And when Galvatron was destroyed, he joined the Autobots, but was forced back into the ranks of the Decepticons by Thunderblast, Ransack and Crumplezone, and went into space. Soon after, they ended up on Mars.
- Thundercracker is first mentioned in Armada, after Starscream gains a blue colour scheme in the "Unicron Battles", with Starscream remarking on his similarity to Thundercracker.
- In US Armada fiction, especially the Dreamwave Comics, this Starscream recolour was depicted as it's own version of Thundercracker, who was characterised differently to the jokester of Cybertron. As the Armada animated series was made in Japan, the Thundercracker Starscream is reffering to is likely the Cybertron character, although at the time, the Thundercracker mention was meant to align the two different uses for the "blue Starscream" look.