In "A Fistful of Energon", Optimus Prime is informed by Ultra Magnus about Starscream's escape from prison. He is quite upset when he has heard that Prowl set out in search for him on his own. He orders Prowl to return, but he disobeyed him. Later, Prowl is bound and abandoned by Lockdown, who wants to get the bounty that Megatron had set on Starscream. But Optimus Prime, together with Bulkhead and Ratchet, succeed in finding and releasing Prowl.
The Autobots helped repair a Smitco Oil Refinery site which the Lazarus-controlled Transformers had attacked. Optimus had no answer for Spikes accusation that the Transformers' presence on Earth was responsible for the destruction. When Megatron's activities at Lazarus's base were spotted by the military, Optimus insisted on the Autobots going in without backup. They discovered Megatron in the middle of a plan to reformat Earth into a new Cybertron using a cyber-virus. Optimus rejected Megatron's suggestion he should just let it happen, but while the two factions fought, the human military unleashed Operation Clean-Up, dropping a bomb on them. Prime Directive #3
In "The Elite Guard", the Autobot Elite Guard, composed of Ultra Magnus, Jazz, and Sentinel Prime, arrive on Earth to reclaim the Allspark. They don't believe Optimus' story about the Decepticons and Sentinel Prime wishes to have him court-martialled. When a fragment of the Allspark causes a production line to go haywire, Optimus finally stands up to Sentinel, retrieving the fragment, and earning praise from Ultra Magnus.
Based upon the "Protoform" (Cybertronian) appearances of the Transformers in the Movie, Protoform Optimus Prime transforms into his "entry" mode. This mode somewhat resembles a cybertronic truck, with false wheels sculpted onto the sides, and Optimus Prime's trademark windows in front. A flame decoration piece fits to the back of the "vehicle", creating the illusion of a flaming comet's tail. The bottom of the vehicle has small wheels to roll the toy across smooth surfaces. Oddly, it has NO automorph gimmick at all, a feature most main-line figures have.
The first Generation 2 Optimus Prime toy was largely identical in sculpt to the original release. However, his trailer was cast in black plastic, with the original blue and silver striped sticker replaced with a red and silver one that had "Optimus" in large block letters on it. The trailer also featured a soundbox attachment with a sculpted Autobot symbol on the front. The soundbox could activate a truck engine noise, a laser gun sound effect and a (badly) garbled voice that said "I am Optimus Prime!". This soundbox could also be attached onto Optimus Prime's back and be used as a sort of backpack.
When Sideswipe was accused and convicted of destroying the Nova Suspension Bridge, Optimus was infuriated that one of his own Autobots could commit such a heinous act. Optimus was tasked to hunt down and deactivate Sideswipe, though the task proved to be easy as Sideswipe did not run, hide or resist. After Optimus had deactivated Sideswipe, he was approached by Prowl, who pointed out that Sideswipe's actions made little sense, as he had committed the crime in broad daylight before many witnesses. Agreeing that the Decepticons might be behind the situation, Optimus allowed Prowl to take a team of Autobots to Carob Island to clear Sideswipe's name while Optimus and Jazz stayed behind to continue working on human/Autobot relations. Prowl returned with evidence that it was indeed a Decepticon-controlled clone of Sideswipe that had committed the crime. Optimus then presumably reactivated Sideswipe when his name was cleared. Deadly Paradise