Rodimus was seen in the season 3 "Transwarped" special, leading his team in defending a Space Bridge from Strika's "Team Chaar". His team was overwhelmed, and Rodimus is infected with Cosmic Rust, courtesy of Oil Slick, putting him out of commission. According to Derrick J. Wyatt, Rodimus is back on Cybertron de-rusting. He can later be seen on Cybertron cheering for Optimus Prime and his crew for defeating the Decepticons in "Endgame, Part II".
Optimus had Bumblebee and Huffer plant false information to mislead the Decepticons. As the Autobots were in need of a new power source, he sent Cliffjumper to find Doctor Heath Blaisedale and had to apologize to the doctor after Cliffjumper kidnapped her. Persuading her to help them, the Autobots traveled to the solar plant to make use of her solar reactor, only to find the Decepticons were already planning to attack it. While the other Autobots re-energized, Optimus protected them from an attack by Starscream, Thundercracker and Skywarp. Ravage abducted Blaisedale as a diversion, forcing Optimus to lead a team and rescue her. When the team returned, the plant was already under attack and Optimus helped the Dinobots drive them off. Unfortunately the Dinobots totaled the plant in the process, and Optimus promised Blaisedale the Autobots would help her rebuild. In return, Blaisedale organized a meeting with the President of the United States so the Autobots could forge an alliance. Sun Raid (Listen 'n Fun)
In "Sick Mind", Optimus is infected with the life-threatening Cybonic plague, prompting Arcee and Bumblebee to infiltrate the Nemesis to find a cure for the virus Megatron himself created. As Optimus grows weaker, he learns of Megatron's survival of the space bridge explosion. It was Bumblebee entering Megatron's mind via cortical psychic patch and retrieving the cure that saved Optimus. In the next episode, "Out of His Head", Optimus is, surprisingly, saved by the revived Megatron when he intercepted Starscream's attempted nosedive to kill him.
Within G.I. Joe's headquarters, Optimus found Doctor Venom controlling a robotic suit made out of the remains of both Bumblebee and Soundwave. The battle between him and the Joes spilled out into the open and into another battle, where Decepticobra was attacking the United Nations. As more factions joined the brawl, Optimus yanked Bumblebee's components free from Soundwave's body and took to the skies, back to Cybertron. Expelled from the Garden There, he was able to reunite Bumblebee's body with his head. Headmasters
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.
If Optimus ordered his troops to come to the humans’ aid, they found themselves taking part in a struggle in futility, as the entire town was near-weightless, meaning they couldn’t put the humans anywhere where they wouldn’t float away once more. Then, the Autobots heard Decepticons approaching. Helpless in their current position, the Autobots were quickly eradicated by the Decepticons.