Dark Awakening

An Autobot shuttle containing Rodimus Prime, Ultra Magnus, Kup, Arcee, Spike and Daniel is being hounded by the Decepticons, the Quintessons having led them there, while Galvatron blasts their communication screen just because he can. Although the Autobots shake them slightly by entering an asteroid field, it doesn't stop them for long, and the Decepticons use the opportunity to fire homing torpedoes.
 

The Autobots pull the same separation trick they used in the movie (though Rodimus is the one to suggest it; Ultra Magnus probably couldn't deal with that now), though at the loss of communication and a great supply of air for their human comrades, allowing Rodimus to be a pessimistic ass while suggesting they land at whatever's up ahead. On closer inspection, it turns out to be a tomb for all the Autobots they lost in the great war, so although they've got somewhere to land, it's not exactly a place they wanted to see again.
 

While everyone leaves the ship and go walking about, Daniel goes about looking at the tombs for some of the Autobots, but after accidentally turning the lights off and on again, he sees a brutal rendition of a familiar face and makes a run for it, nearly getting crushed by an empty chassis before meeting up with the others and telling them of who he saw. They refuse to believe his tale, though Rodimus wants to know for certain, so they approach Optimus' tomb and after a moment of hesitation, open it to reveal...

Nothing! Rodimus then inexplicably believes the Decepticons are here, and he's right, somehow, as Galvatron and his homies have arrived and are attacking, destroying their shuttle and forcing them back inside and into defenceless situations, but when it looks like they're all toast...

It's Optimus Prime!
 

The former Autobot leader blasts at Galvatron, weakening him and forcing the Decepticons to fall back, allowing the Autobots to rush 'em and make them leave; all thanks to Optimus. Rodimus is more than happy to return the Matrix of Leadership to him again, though the others are a little wary, what with him being dead for years.

Optimus' explanation for his revival is just mutterings of the words "darkness," "cold" and "light," which leads Daniel to believe he was merely comatose, while Optimus mutters something about completing a plan while returning to the docking bay, revealing that he had built himself an escape ship.

Rodimus takes this as him still being his old resourceful self and forces the Matrix into his hands after some signs of resisting and reluctance from the dead guy. Hot Rod makes it clear that he has a different personality than Rodimus Prime before Optimus apologises to his buddies while drawing a rifle and blasting Hot Rod in the chest.

Unsure of what he just committed, Optimus activates the auto-destruct sequence on the tomb and makes a getaway in his ship, leaving the less-prepared to sit around inside still thinking that Optimus is a good guy, even though they're either going to explode first or crash into a nearby sun.

Optimus returns to Cybertron to tell the citizens that everyone aboard the tomb perished so that he could survive, claiming the Quintessons took no prisoners. Grimlock is pretty moody about this and spends almost a minute thumping his tail against the ground, while Springer is more cheesed off about Arcee getting toasted.
 

However, this proposed attack against the Quintessons by Optimus is just a ploy by the very creatures they attack, who plan to completely obliterate the Autobots in the process!

Meanwhile, those aboard the tomb manage to conveniently find another shuttle and escape as the tomb is destroyed, along with all the deceased heroes lying aboard, while they set course for Cybertron.
 

And by set course, I mean crash straight into one of the command towers, manned by Snarl and Sludge for some reason. They're not happy to see the very people that Optimus claimed were dead, leaving them rather confused, though they remain non-violent enough to explain that Optimus has taken the whole fleet with him to fight the Quintessons.

The former leader leads them to a planet that he claims is the Quintessons' new base, refusing to send scouts and believes that having the whole army rush in is an element of surprise. Blurr, however, informs him that those he said were dead have actually arrived safely on Cybertron, which he dismisses as a Quintesson trick. Meanwhile, the Quintessons reveal that the planet is a decoy, and Prime still has no idea what's happened to himself.

The Quintessons then strike, moving their asteroid ships in to fire missiles and more or less decimate the Autobot forces, chuckling and snickering over how utterly simple it is to blow those guys up good. Don't worry, they're all generic guys. Nobody important is dead!

Ultra Magnus calls the flag ship and tries to order them to call off the attack while asking for permission to board, but Optimus just orders his crew to try and destroy the ship. The crew aboard it are sucked out into space before it explodes, allowing Perceptor to see the said-to-be-dead guys and orders them to be rescued. The Quintessons still believe things are going swell, claiming their rescue will only confuse the Autobots...

After all, they only need to fly on for a while longer to reach the detonator, where they'll just be exploded into oblivion along with two nearby planets. On board the flagship, Hot Rod demands they turn the ship around while he makes a door explode simply by punching it, looking for Optimus.

Hot Rod claims he's taking command, which only causes Optimus to grunt some more while clutching his head, flashing back to whatever dastardly deed was done to him: The Quintessons retrieved his body and fixed him up to operational status, but without his original programming, he will merely be a robotic zombie. Hot Rod tries to help his unwell leader...

Only for Optimus to start firing at him again. Hot Rod hides in the fog to fool him and make him drop his gun, but he only sets himself up for some knuckle sandwiches before becoming a victim of attempted tearing apart.

Hot Rod shakes him off and manages to hurl him against a wall, dislodging Prime's arm, but that doesn't stop him from thumping Hot Rod with his mighty boot, demanding to know why he didn't simply finish him off. However, before he can blast him away, Optimus' former self is reawakened by the exposed Matrix, who returns it to Rodimus and is disgusted at the Quintessons for programming him to destroy the ones he loved most of all.

Optimus leaves before Ultra Magnus, Kup and Arcee arrive to get Rodimus off the ship, while the reformed Autobot leader takes control of the ship to tell everyone aboard to return to Cybertron, and that will be his final command. The Quintessons are surprised at the Autobots' retreat, but notice that the flagship is still heading towards the detonator.

The Quintessons start firing away upon it, damaging it severely but Optimus still struggles onward, ploughing through the defences, and utters "'til all are one" once again before hitting the detonator, destroying all of the Quintesson forces along with himself.

The Autobots, shaken by their reuniting with their old leader, bid farewell as the explosion dies down, Rodimus promising that although he may never be the leader his predecessor was, but he'll try his best to live up to him.

"So long... Optimus Prime."

Most depressing episode ever!

Production order and broadcast dates put this fairly early on in the series, but The Return of Optimus Prime retcons the ending pretty severely, axing the Quintesson ambush and every heart-rending element about the episode to make it so Prime is just sitting in the shuttle, deactivated and in mint condition, about to crash into a sun.

The only Autobots Daniel reads out in the tombs are the first four to die in the movie, but replacing Brawn with Huffer, strangely; the only other casualties seen, Wheeljack and Windcharger, go unmentioned.

Jazz makes a brief one-scene cameo, coloured like Blurr.

I mention this because seriously, Bumblebee is the only survivor of the movie to actually do anything. =(