Leading the defense of the city when it came under Decepticon attack, Magnus suddenly found himself commanding the entire Autobot army when Optimus Prime died in battle and passed the Matrix of Leadership to him despite his protestations. Subsequently, in a confrontation with the Decepticons on the planet of Junk, Magnus was blown apart and lost the Matrix to Galvatron, but was reassembled and reactivated by the Junkions.
When Hot Rod recovered the Matrix from Galvatron and became Rodimus Prime, Ultra Magnus decided to step down as leader to give the role to Rodimus, but continued to act as his friend and advisor, keeping him on the straight and narrow and always reassuring him, attempting to urge him out of the shadow of Optimus Prime.
Magnus had his share of personal adventures in 2006, such as when he was captured by a Quintesson scientist for study, along with Wreck-Gar, Marissa Faireborn and the Decepticon, Cyclonus; he and Cyclonus developed a mutual, grudging respect for each other as warriors during the ensuing events, as they worked together to escape a negative universe on the other side of a black hole.
Magnus would later fall afoul of an unrepentant Cyclonus when he went to the aid of Wheelie and Daniel Witwicky when they stumbled into trouble while attempting to discover Magnus's birthday. In addition to these and other battles with Cyclonus, Magnus also found himself facing Galvatron on several occasions - the deranged Decepticon would even occasionally focus his rage more upon Magnus than Rodimus Prime; such a notion is not inappropriate, since Magnus was the being he was originally dispatched to destroy, and who thwarted him in varying ways, certainly enough to permanently earn the deranged Galvatron's ire.