Major Story Arcs
Marvel Comics Continuity
As a candidate for leadership of the Decepticons on Cybertron, Thunderwing's final test was to hunt down and kill three Autobot prisoners released on Earth to provide fodder for the test. While Thunderwing killed two of his targets, additional Autobots came to the third's aid and he was left temporarily deactivated at the bottom of the sea. He later resurfaced, and when a squad of Decepticons arrived to bring him back to Cybertron he beat them into submission and forced them to accompany him as he attempted to avenge himself upon the Autobots by attacking them in the Autobots' ship, the Ark. Although he was unsuccessful in getting his revenge, Thunderwing's boldness and single-mindedness in commandeering troops sent to capture him and in attacking the Autobots' stronghold with such a small force impressed the Decepticon high command and he was thus appointed leadership of the Decepticon faction on Cybertron.
While he was seen sending assassin to eliminate the Autobot heroes Jazz, Bumblebee and Grimlock, it wasn't until the Matrix Quest that Thunderwing became truly prominent. Learning that the planet-devouring entity Unicron was heading towards Cybertron, and that their best bet for stopping him was their lost Creation Matrix, the Autobots dispatched several squads to search the stars for the lost heirloom. Thundering developed both a mental link, and a growing obsession with the Matrix, his connection to it convincing him that he was destined to possess it and he stalked the searching Autobot squads. He was eventually successful in this endeavour as he overpowered and incapacitated an exhausted Jazz, Grimlock and Bumblebee when they found the Matrix.
This proved a something of a poisoned chalice, as the Matrix soon came to possess Thunderwing, the relic having grown fascinated by the concept of evil after being owned by pure, good hosts for so long. In a confrontation with Optimus Prime, Thunderwing was harpooned and shot out of an air-lock while still possessed by the Matrix, the spirit of which had manifested itself as a horned demon. The tainted Matrix returned later during the Transformers battle with Unicron with the possessed Thundering it tone. It attacked Unicron as it wanted revenge on the Autobots who defeated it. However, its manifested demon form was destroyed by Unicron, as it was the Matrix purity and goodness which threatened Unicron before, and its pursuit of evil made it less potent to him. Thunderwing was destroyed as the Matrix's manifestation was.
Afterwards, Optimus Prime reacquired the Matrix, purified it through force of will then used it to destroy Unicron.
Despite being a Decepticon Pretender, Thunderwing was never seen outside of his shell during the Comics US run, though he did exit it briefly in one of the British comics.
IDW Publishing Continuity
Thunderwing was a Decepticon scientist who saw that the war between the Autobots and Decepticons was destroying Cybertron. He tried to warn scientists on both sides that the war and leeching of all available resources had shattered the planet's protective atmosphere and ravaged its ability to restore and replenish itself. He said that now all that can be done is they can minimize the planet's collapse and do what they can to survive. Unfortunately, none would listen to him so he ultimately took matters into his own hands. He would attempt to undergo a bio-cybernetic grafting process but the neuro-shell's symbiotic fusion would destroy his mind and drive him mad. He would then go on a rampage, leaving the planet a barren wasteland. The Autobots and Decepticons joined forces to try to stop him but ultimately the planet itself would rip open and swallowed Thunderwing whole, as though it was bent on one last selfless act of sacrifice.
Thunderwing's body would remain dormant and buried deep within Cybertron at a place known as Thunderhead pass. However, his body was soon discovered by Bludgeon who believed that Thunderwing could be used to revive Cybertron by burning other planets in hopes that it would soothe the spirit of the planet. Bludgeon would re-power Thunderwing with ultra-energon and since he knew Thunderwing couldn't be controlled, he instead decided to just direct where he'd go. Thunderwing would go to Nebulon and he would terrorize the planet. Here, a group of Decepticons would try to stop him, since they controlled the planet and didn't want to lose it, but they were all easily overpowered by Thunderwing. Meanwhile, back on Cybertron, Optimus and the Wreckers would go to Thunderhead pass where they would destroy the axis cradle which directed Thunderwing. With this, Thunderwing would leave Nebulon and head back to Cybertron where Aubots and Decepticons would attack him to no avail at first. However, after learning that Thunderwing was powered by ultra-energon and learning about how it is only meant to take short, intense hits, a massive assault is led against Thunderwing, forcing him into a secondary ultra-form. Ultimately, Thunderwing would be brought down by Optimus, who said that Thunderwing may have seen what was happening to the planet but his actions only facilitated its destruction and that facing him and returning to Cybertron helped him to finally accept his mistakes.