The Animated Movie

What began as fishing trip with Daniel Witwicky, son of human ally Spike ended as unwanted discovery for Hot Rod when he and Daniel spotted a hole in Autobot ship with Megatron and his Decepticon contingents inside. Hot Rod fired, only to make matters worse as Megatron and his main strikeforce launched into full-scale attack on Autobot City and surrounding areas. 

Outnumbered and completely unprepared, stand-in Autobot City commander Ultra Magnus instructed Perceptor to contact and get Blaster to relay a broadcast message to Optimus for reinforcements while he and new Autobots Arcee, Springer, Kup and Blurr tried to delay Decepticons' siege. Hot Rod and Kup arrived in nick of time to help them only to face another barrier in Devastator - combined giant robot of Constructicons who was instructed by Megatron to tear down Autobot City walls. 

Optimus Prime and his reinforcements of Hound, Sunstreaker and Dinobots of Grimlock, Sludge, Slag and Swoop arrived later. After instructing the Dinobots to destroy Devastator from further Autobot City damage, he went on a solo fight against Megatron and his Decepticons. 

Just when he had an upper hand on Megatron, he was momentarily distracted by Hot Rod who tried to ambush Megatron from behind. The ploy failed and Megatron ended up killing Prime but not before he was seriously wounded by Prime and discarded into space by Starscream later along with his damaged Decepticons of Skywarp, Thundercracker, Bombshell and Insecticons. 

Despite Perceptor doing his best, he could not save Prime as he was a scientist and not medic. Moreover Ratchet also perished in earlier attack and Protectobots were not present as they were defending the first Ark against Bruticus and Menasor alongside Superion. Before his death, Prime passed the Matrix Of Leadership to Ultra Magnus - who was the largest and strongest of all Autobots. 

Just when death seemed imminent for Megatron and his seriously wounded Decepticons, they were resurrected and modified into Galvatron and Sweeps but under one condition by Unicron to find and destroy the Autobot Matrix Of Leadership which Unicron perceived as a major and only threat to his existence. 

Galvatron and his forces returned to Cybertron, killing Starscream who proclaimed himself as new Decepticon leader. He followed up with another attack on now ruined Autobot City where Ultra Magnus and his Autobots escaped in Ark-II. But when Decepticons' attack intensified and Autobots' firepower and fuel running low, Magnus decided to split the ship into two. One containing him, Arcee, Springer and Daniel while the other with Hot Rod, Kup and Dinobots. Both ships crashlanded on planet Quintessa and Junkion. 

On Quintessia, Hot Rod and Kup learnt from fellow prisoner Kranix who turned out to be the last survivor of Lithone. After he was executed by Sharkticons - deadly guards and alligators of Quintesson Masters and the same fate was about to happen to Hot Rod and Kup, Dinobots arrived to save them. 

On Junkion, Ultra Magnus sacrificed himself to save his remaining Autobots after being gunned down and stripped of Matrix by Galvatron and his forces. He was later rebuilt and resurrected by Wreckgar and Junkions after an initial misunderstanding battle. 

Galvatron attempted to activate Matrix to destroy Unicron but ended up at his mercy when Unicron revealed his true form by transforming into giant humanoid robot. Unicron also destroyed Cybertron, killing Shockwave and most of his elite Decepticons. 

Just when all hope seemed lost, Hot Rod accidentially activated the Matrix and Optimus' disembodied voice, becoming Rodimus Prime and next Autobot leader. With his Autobots' and Dinobots' help, they destroyed Unicron and retake Cybertron as their home planet. 

But Unicron's soul still remained in decapitated head flowing in space towards the end of the movie.