It is not clear, but Ultra Magnus may have formerly been Dion, the best friend of Orion Pax, the robot who would become Optimus Prime. Whatever his origins, Ultra Magnus made his first appearance in 2005, amidst the chaos of the Autobot City Massacre. Magnus had been appointed commander of Autobot Ciy by Prime, who was at the time on the first moon of Cybertron, preparing a strike on Cybertron itself to free it from Decepticon control. When Decepticons attacked and boarded the shuttle which was headed for Earth from Moonbase One, they layed seige to Autobot City. When Prime arrived on earth and engaged Megatron in battle, both leaders inflicted mortal damage to eachother. However, Optimus Prime succumbed to his wounds first, and passed the Autobot Matrix of Leadership on to Ultra Magnus, making him the Autobots' new leader.

Ultra Magnus transforms into the likeness of an Earthen vehicle transporter, capable of carrying his fellow Autobot cars. In both robot and transporter mode, he is equipped with shoulder-mounted twin missile launchers, and in robot mode, an additional standard blaster. Ultra Magnus is more comfortable when taking orders, rather than giving them out. He likes his position as a soldier, and does not enjoy the prospect of leading. His name means "Beyond Greatness" in Latin.

Ultra Magnus's stint as Autobot leader had only just begun when a communication from Moonbase One was recieved on Earth - a monstrous metal planet known as Unicron was heading towards Cybertron, consuming all in it's path. With only Prime's last few words to guide him - "the power of the Matrix shall light our darkest hour" - Magnus ordered the Autobots to prepare shuttles to head for Cybertron and stop this menace. However, before they could blast off, the Deceptcons attacked again, now led by Galvatron, who was actually Megatron, rebuilt into a new form by Unicron. Magnus boarded a shuttle with Arcee, Springer, Blurr, Perceptor and Daniel Witwicky, and blasted off alongside the other shuttle, piloted by Kup and Hot Rod, who had the Dinobots along with them. The Decepticons managed to track them down, and Hot Rod and Kup's shuttle crashed to the planet of Quintessa. Magnus used the ship's auto-destruct to detonate three-quarters of his shuttle, fooling the Decepticons into thinking they had destroyed them. Perceptor then sat the shuttle down on the planet Junkion, to repair the damaged craft. While on Junkion, the Autobots were again located by the Decepticons, and Ultra Magnus tried to open the Matrix to save them. The Matrix refused to open, and at Galvatron's command, the Sweeps blasted Ultra Magnus, who exploded into millions of pieces.

Galvatron stole the Matrix, and destroyed the Autobot shuttle, leaving them stranded. Then, the Autobots found themselves attacked by the Junkions, a race of robotic creatures whose bodies were comprised out of junk. Springer was nearly scrapped by their leader, Wreck-Gar, but Hot Rod, Kup and the Dinobots arrived in a stolen Quintesson ship and used the famous Universal greeting to make peace with the Junkions. The Junkions then rebuilt and reactivated Ultra Magnus.

When the Autobots journeyed to Cybertron to try to stop Unicron, it did not appear that Ultra Magnus voyaged inside the planet eater. While inside Unicron, however, Hot Rod retrieved the Matrix from Unicron, and was proven to the Autobot Prime had spoken of - the chosen one, who would rise up from the Autobot ranks and use the power of the Matrix to light the Autobots' darkest hour. through the power of the Matrix, Hot Rod became Rodimus Prime and used the Matrix to destroy Unicron utterly, from within. Rodimus took over command of the Autobots from Magnus.

Ultra Magnus became second-in-command of the Autobots in 2006. Despite his supposed dislike of being in a position of leadership, he often nagged Rodimus for being immature or joking around, always suggesting how he could do things better. Truth be told, however, Magnus thought Rodimus to be a more than suitable replacement for Optimus Prime. Magnus was always seen in the midst of battles, and apparently killed Ramjet, by shattering his nosecone and guidance system with one punch, sending him crashing into a tower, where he exploded, during the Battle for Cybertron. Ultra Magnus's fate following the restoration of Cybertron's Golden Age is unknown.