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Landmine's first use of his Cyber Key, and his "Cyber Tempest" attack.
Vector Prime using his Time Reverse power for the first time, to save the human kids and Minicons from destruction.
Vector Prime: They were destroyed because I left them... No! This will not stand. I am a keeper of space and time. I can see through time. I will travel through time. I can change time. I will change time!
The ancient Cybertronian starship Atlantis rising from it resting place on the ocean floor.
Optimus Prime retrieving the Omega Lock, and escaping from the self-destruct of the Atlantis' treasure room.
Overhaul's rebirth as Leobreaker.
Optimus Prime and Leobreaker linking up into Savage Claw Mode for the first time, and handing Megatron his aft.
Hot Shot winning the final race against Override, with the help of Coby riding in his cockpit manually holding together a systems bypass.
Everything from when Lori confronts Scourge about his beliefs to his handing the Jungle Planet's Cyber Planet Key to a victorious Optimus Prime.
Red Alert, Hot Shot, and Scattorshot bringing themselves back to life through sheer will.
Primus transforming from the planet Cybertron.
Optimus Prime battling Megatron in the latter's personal dimension. The fact that they both unleash a full-on No Holds Barred Beat Down on each other, in this midst of a place that looks like a Fire and Brimstone Hell makes it even more so.
TFWiki.net actualy compares this scene to the image of a hero battling a demon in the depths of Hell.
The Autobots were fleeing Earth with the Omega Lock and Cyber Planet Keys via a space bridge, when Starscream shows up, smashes through the lot of them with a Foe-Tossing Charge (getting one of his blades snapped off in the process) and finally gets his hands on the Omega Lock when Optimus Prime shows up for round 2. Starscream takes everything Optimus throws at him, and in the fight he and the Omega Lock get thrown off the space bridge. As Optimus dives for the Omega Lock, Starscream realises Optimus' one weakness, and fires a missile at the kids, who were watching from the ground. Optimus dashes off to save the kids, whilst Starscream swipes the lock and keys and hightails it out of there.
This is made more epic by the underlying symbolism. In a series where damage is rarely shown and even scorch marks indicate getting hit hard by a strong attack, Starscream is covered in cracks on his physical armor and short-circuits all over his body - even before fighting Optimus Prime. He has lost one of his arm-blades. This would be the equivalent of a human having deep bleeding gashes all over their body and a bullet or three lodged inside them somewhere. Despite Starscream otherwise being a fan of the Villain Exit Stage Left through his dimension gates, he fights on. The attack Optimus Prime then uses on Starscream has won every other time, including against Starscream's boss Megatron, and at that point in the show has no effective counter. Starscream (unsuccessfully but epically) meets it head-on by channeling all his remaining power and declaring "The power...IS MINE!". After the ultimate attack overwhelms him, Starscream's eyes dim, indicating unconsciousness (which for the setting is implicitly very near death). He reactivates through near sheer will. And wins his ultimate objective (admittedly with a cheapshot that may have crossed the Moral Event Horizon).
Optimus Prime and Wing Saber making their way through Starscream's swarm of boulders, and then linking up into Sonic Wing Mode for the first time on-screen to take him down.
Metroplex, being larger than any other not-planet transformer in the series, curbstomps Megatron. Literally. And shrugs off several of the other Decepticons trying to help in the process. Then when Megatron finally knocks him off, he slams him through SEVERAL FLOORS with one strike of his just-as-tall-as-he-is battleaxe.
Megatron's revenge. He calls upon the Cyber Planet Keys to become Galvatron, and hands all of the Autobots their tailpipes singlehandedly - even Metroplex, whose ankle he barely comes up to. While giving Shout Outs to Transformers: The Movie. ("Such heroic nonsense!")
Landmine temporarily becoming giant and getting back at Starscream.
Optimus finishing the subsequent beatdown of Galvatron with Metroplex's giant axe.
Galvatron's showdown with Starscream. It is truly epic. And Starscream almost WINS the battle.
The Giant Planet trio get a group CMoA. A massive chunk of rock knocked loose by the Galvatron/Starscream duel threatens to fall on the kids. First Quickmix and Menasor jump at it in unison and use their giant spinning drill/drum appendages to cut it down to size, and then Metroplex shields the humans from the remaining debris with his own body. And still has something witty to say afterwards.
The final battle between Starscream and Galvatron. Galvatron gets a villainous Heroic Second Wind and unleashes his full power on Starscream, with Starscream responding in kind, both deploying Battle Auras. Other Characters note that they're channeling enough energy to wipe out a small planet. Fortunately, they are on a very large planet. Both of them attempt to punch the other, and the result is a Sphere of Destruction which blows a massive crater in the planet they are fighting on and blasts Starscream into another dimension, which he implicitly returns from after the series.
Optimus Prime: Only one shall stand, Galvatron. It ends here!
They charge at each other, clashing for the absolute final time. Galvatron lifts his sword and swings at Optimus. Optimus dodges, and rams Rhisling through Galvatron's own blade and then through Galvatron's spark core. A shard of Galvatron's smashed blade shatters Optimus' faceplate. There is dramatic smoke. When it clears, Galvatron's final words are the second homage.