Scorponok tries to use a sword formed from Megatron's own spark to put an end to him for good. It appears that he can't fight back on account of being a corpse stuck in a wall, but at the last moment, Megatron absorbs the sword back into himself, siphons energon from Unicron's own body, and bursts out of his old form in a kick ass new form. Then he proceeds to beat the living hell out of Scorponok, and then once he's a quivering heap on the floor, he effectively brands Scorponok with the Decepticon symbol.
A more subtle awesome would be Starscream kneeling and apologizing to Sixshot to spare Galvatron the humiliation of doing it himself, before Galvatron even has a chance to respond.
Demolishor knocking Megatron out of the way of the Energon Field, when he had previously doubted him.
Inferno fighting off Megatron's mind tainting power for several episodes, (failing eventually,)and sacrificing himself. And then he comes back, rebuilt as Roadblock, riding upon one out of many Energon Towers.
Small moment for Scorponok who, following Inferno's breakdown, saves Starscream from falling into an Energon sun.
Scorponok's toy from this series was a masterpiece.
Scorponok saving Galvatron from Sixshot'srevenge attack (which itself could be considered somewhat impressive amist Sixshot's weaseliness, given after spending most of his run in the show being smashed into his own control booth, he semi dismantles Galvatron with his laser with ease, considering most Transformers couldn't even dent him).
The episode prior to this, Sixshot attempted to thrust Cybertron's speed by blasting the energon grids to thrust it forward. When the Autobots intervened (leading to a gargantuan Energon-powered Optimus), Galvatron starts blaming Sixshot for things going wrong and demands he increase the Energon level to dangerous levels. When his warnings are ignored, Sixshot snaps and sets it full power...and doesn't stop...intentionally letting the planet overload while sneering verbal abuse at his Bad Boss over this horrid strategy. He naturally reverted to normal weasel mode when a physical confrontation occurred, but for that brief moment, Sixshot was willing to destroy the entire battlefield just to point to Galvatron's face how stupid he was.
The final fight between Unicron-powered Optimus and Galvatron, helped by the Art Shift to much better looking cel animation.
The battle between Unicron and a planet-size Optimus Supreme. Especially the final attack from Optimus.
This continuity's Starscream proves how he differs when Megatron's methods reach their extremity. Optimus Prime warns Starscream that Megatron is about to tear the universe apart with Unicron. Both the latter and Mirage scoff that Prime believes they'd disobey him just with that notion. They follow Megatron to the bitter end.