Prime would make one further surprise appearance in Dreamwave's Transformers: Armada series. With Optimus Prime having disappeared to an alternate dimension, devastated by Unicron, the Autobots attempted to find their leader. As Jetfire attempted to locate him through Spacebridge links to other dimensions, one of these clearly shows RiD Optimus Prime and Prowl.
Optimus found himself carrying into battle many miniature robots and machines to the battlefield in the palm of his hand. Among these was a Micromaster city, Micromaster micro bases commercial, the Race Car Patrol, Micromaster Patrols commercial and the Hot Rod Patrol. He and Jazz checked out the Hot Rod Patrol, and Optimus wondered if they could transform. Hot Rod and Construction Patrol commercial
Optimus Prime was given the Matrix by Primus himself, and used to be friends with Megatron. Prowl is his closest friend and Ratchet is his oldest. Searching for Energon, the Autobots landed on Earth, but were followed by the Decepticons. With the help of their human allies, they bested their foes, and knowing they would return, decided to stay and wait to defend the planet once more. Optimus Prime was proud to be an Autobot. I Am Optimus Prime
Thanks to Hasbro on their official site, which can be accessed by clicking any of the images below, we have news of 2 new members of the Energon Igniters class of figures, along with new images of 3 more! Up first, we have the 2 new reveals: Power Plus Soundwave and Ironhide! Soundwave looks a lot like he did in the movie, with a G1-esque robot mode, and a new van mode that is very Animated-esque, complete with a totally metal image of a jaguar and bird of prey on the side, evoking - Read More
Commander class figures all come with translucent weaponry, and feature some amount of translucent plastic in their bodies (blue for Autobots, but a variety of colors for Decepticons), a feature designed around interacting with the line's vehicles (see below). Each vehicle is equipped with an "Energon Booster", a light-up accessory that can plug into the Commanders' weapons or into the posts and ports on the figures' backs to illuminate them with "glowing energon power".
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
The third version  would quite possibly have been the most gimmick loaded Transformer in the history of the line, simultaneously being a Powermaster, Headmaster, and Triple Changer. The Headmaster also would have been a Triple Changer, turning into a sort of armored four-wheeled rover (Roller II?) and robot as well as a rather silly looking Optimus Prime head with four vertically aligned wheels jutting off the sides. It seems that when the extra Headmaster gimmick was scrapped, the super mode head remained separate rather than being reintegrated into the trailer hitch such as on the earliest design. Notably, the body of this design is extremely close to the final design.
After the successful Armada toy line, Hasbro/Takara introduced Transformers: Energon. The accompanying television series program was a direct continuation of the events of Transformers: Armada and featured many of the same characters in new forms. This was reflected in the toy line, as characters such as Hot Shot, Jetfire, Optimus Prime and Megatron were all released with entirely new molds.
Transformers GT "GT-R Prime" is a heavy retool of Alternity Convoy, transforming into a 1:32 replica of the Motul Autech GT-R race car used by the Nismo team in the Super GT racing championship series. He retains the flip-out blasters of the Alternity toy and can also wield his new Impact Wrench Gun accessory (also called the "Optimus Rifle" on the Transformers GT website), a weapon based on the impact wrenches used in car repairs. Like all GT toys, Prime also comes with a GT Sister, poseable human figures themed after race queens, his partner being a lady named Misaki.
On a Cybertron dominated by Shockwave and the Decepticons, Optimus Prime and the Autobots took on the roles of resistance fighters. Cobra experimentation transported a contingent of Cobras and G.I. Joes to Cybertron and destabilized Teletran 3, which led to the computer sending several Transformers to Earth across different time periods. When Optimus Prime saw Jazz get zapped by Teletran 3, he leapt to rescue his soldier, only to be transported away as well. G.I. Joe vs. the Transformers II #1 A team made up of Joes and Cobra agents were sent back and 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. G.I. Joe vs. the Transformers II #2
Just which character this toy represents is up for debate. The toy's bio claims he used to turn into a tractor-trailer (indicating Optimus Prime), but considering the timeframe of when they were written and the whole lack of a stance on who Primal "was" before the show and blah blah blah... it's just easier to file this under the same iffiness as the original toy bios set on modern Earth and leave it at that.
Optimus made his way to the Primal Basilica, where he found Perceptor standing over the Mistress of Flame's battered corpse. Unable to do anything for her, Prime activated the Basilica's defenses as a means of stalling Trypticon. Learning from Perceptor that Rodimus had given up the Matrix, the two entered the chamber of the Chorus of the Primes to have the Matrix returned to him. Desperate Actions However, Optimus revealed the Matrix was not for him, but rather for Perceptor, as he wanted to make sure it would be taken as far away from Trypticon's grasp as possible. He guided Perceptor to a secret exit from the Basilica and sent the scientist on his way. Run for Our Lives Warned by the Chorus to "beware the power of the Primes", Optimus charged back towards the battlefield and began attacking Trypticon, rescuing Victorion. Optimus led the Combiners in battle against Trypticon, but the Titan managed to hit him, sending him hurtling towards some sharp rubble. Thankfully, he was caught at the last moment by Fortress Maximus. In Good Hands