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Marvel comics continuity
Optimus Prime noted the creation of Power Station Alpha and ordered Bumblebee to spy on the launch of Alpha, lest the Decepticons try to capture it. When Bumblebee reported the presence of the Decepticon Bombshell, Prime dispatched the Aerialbots to aid him. Subsequently Prime was killed. His body was blasted into space by his fellow Autobots.
Some time later, after Megatron bargained with Cobra for a new body, the G.I. Joe team sent a message to Cybertron, which was received by Bumblebee and Prime, who sent a team of Autobots to get rid of Megatron.
Devil's Due G.I. Joe vs the Transformers continuity
The Ark was discovered by Cobra, and all the Transformers inside were reformatted into Cobra vehicles remotely controlled by the Tele-Vipers. Prime was turned into a Cobra Sentry Missile System tank (a 1985 Sears store exclusive red repaint of the H.I.S.S. tank). During an initial attack on a human peace conference, Cobra's remote control of Optimus mysteriously failed. Later at Cobra's island headquarters in the Caribbean, Cobra scientists pulled Optimus apart to find out what was impeding their commands. As this analysis took place, Optimus reverse hacked into Cobra computers until they shut him down in a panic. Despite this, Prime sent a viral message out to hundreds of email addresses that included the coordinates of Cobra's base. The message was intercepted by G.I. Joe who teamed up with Wheeljack and Bumblebee.
After Wheeljack broke the remote control over the Transformers, Prime went after Cobra Commander. More than a bit frightened of a giant robot gunning for him, the human released Megatron, who was trapped in gun mode. Megatron transformed and fought Prime to a standstill until other Autobots came to back him up.
Although he was weak and low on energon, Prime made a last-ditch effort to save the day when he rammed through the wall of Megatron's energon-producing lab. After a quick recharge, Optimus single-handedly smashed the Decepticons, pounded Megatron to the ground, and ripped his fusion cannon off his arm. Prime then teamed up with the Joes and used Megatron's cannon to shoot down the SPS satellite that had gone rogue and was destroying the island.
The Autobots then returned to Cybertron in a second Ark Class vessel, but not before gifting their human allies with a surprising technological boon: The ability to build and use mecha based on Transformers technology.
Sadly, Prime's homecoming was not all he had hoped for: the Decepticon Shockwave had taken control of the planet. Prime and the other Autobots were forced to go underground, waging a guerrilla war against the Decepticons. Around this time Cobra would attempt to steal Teletran-3, but their attempt to teleport directly into the chamber would set off a catastrophic malfunction, one that threatened to crack open time itself. Cobra experimentation transported a contingent of Cobras and G.I. Joes to Cybertron and destabilized Teletran 3. The computer then sent several Transformers to Earth across different time periods. Optimus Prime and the Stunticons were amongst those who found themselves sent back in time. Teams made up of Joes and Cobra agents were sent back in time, searching for the Transformers. Roadblock, Beach Head, the Baroness and a Viper found Optimus Prime and the Stunticons in 1930s-era Chicago, disguised as period cars and trucks. The Stunticons chased Prime and the Joes around the city until everything was wrapped up with bullets, a collapsed bridge and some dynamite.
After the Transformers and humans were returned to present-day Cybertron and the Decepticons were vanquished by the recently-arrived Dinobots, Prime made an agreement with the Joes to destroy the technology that started the whole mess in order to protect Earth.
In the wake of this incident the Autobots managed to reclaim much of Cybertron. At a peace celebration, Prime was watching a procession of Autobots when Decepticons led by Serpentor attacked. Serpentor's forces proved overwhelming, and Prime voluntarily surrendered to ensure the Decepticons would cease fire. Realizing Serpentor wanted the Autobot Matrix of Leadership, Prime broke free as Serpentor was distracted, but was unable to kill him, promptly being attacked and beaten near death by Razorclaw and Motormaster. He was subsequently forced to watch as Serpentor opened the Matrix. The result was not what anyone expected - Serpentor was not only reformatted into a Transformers-size mechanoid but was shown the futility of the fighting by the Matrix. At this point Cobra Commander was able to take control of Serpentor's body, only being defeated by Hawk opening the Matrix, transforming him into a great leader and rendering Cobra Commander comatose. As the Joes prepared to head home, Prime promised to record the Hawk-led humans' future.
With the Matrix afflicted Hawk receiving dire visions of a new threat, Prime journeyed to Earth personally, taking Hawk and Flint to Tibet to discover the source of the problem - only to encounter Bludgeon. The two battled, with Prime only being saved by Hawk's intervention. Fighting their way into a secret city beneath the Himalayas, the trio realized the extent of the threat - the impending destruction of humanity by Unicron, and the world being taken over by Cobra-La. However at that point they were discovered by Bludgeon and a group of Cobra-La troops. Prime defeated Bludgeon, although the warrior plummeted to his death despite Prime's best efforts. Prime, Hawk and Joe Colton then gatecrashed the Cobra-La ceremony to sacrifice Firewall to Unicron in Prime's truck mode. Prime was then mobbed by Cobra-La warriors, and pinned down by a monstrous insectoid creature. Prime demolished them in time to save Hawk from Golobulus. With Cobra-La arrested by G.I Joe, Prime checked his troops would recover - and then sat down to watch TV with Eject and Firewall.
Sunbow animated series
Even though Optimus didn't find any member of the G.I. Joe team, he once recovered an Oktober Guard top secret jet that had been stolen by the trophy hunter Lord Chumley.
Optimus Prime and Bumblebee were stuck in detention alongside Duke and Snake-Eyes. The Autobots tried to escape switching to transparent forms and the Joes tried to escape by parachuting, but all of them were found by Dr. Mayhem and returned to detention. They were all freed when Mr. Spock teleported Dr. Mayhem to another planet.
(the "massive multiplayer crossover" nature of the Kre-O cartoons allows all these characters to interact without explanation)
- Optimus Prime was voiced by Peter Cullen in the Transformers cartoon. He also reprised the role in the live action movies and their video game spin-offs, the Universal Studios ride, the High Moon Studios video games, the Transformers Prime cartoon and video game and in the Rescue Bots cartoon. Cullen was the voice of Zandar in the Sunbow G.I. Joe cartoon.
- The negative reception of Optimus Prime's death in Transformers: The Movie caused the survival of Duke in G.I. Joe: The Movie.