Ragna's fight with Imego in the final battle. He swordfights the guy to a standstill with his new Cool Sword, pretty much by himself. And it culminates with him nearly killing Imego. Too bad that was his Dying Moment of Awesome.
The Avengers (half of them, anyway) are being completely outgunned and beaten by Samhain. Theron stands up and starts an evolution. Samhain points out his Ancient form won't do it. Theron evolves into ''Azulongmon'' and proceeds to level the whole castle in one attack. Even the unshakeable Samhain was visibly shocked.
The scene when Caesar just turned his Imego form on Samhain, got broken out of it and smashed. He proceeded to interrupt Samhain's corruption chant which would brainwash him again twice. Samhain starts it the third time. Caesar interrupts again, this time with his evolution to Magnamon X. And then proceeds to own Samhain for the first time in the entire RPG.