Dark Is Evil: The story is littered with this reference, from the evil "Black Hands" to the antagonistic Samhain the "Black King" to Hyperion's black-armored evil counterpart, to the title itself.
Divine Date: Hyperion's relationship with Yggdrasil (not to mention Balion's flirting with her).
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Godhood Seeker: Dracul Samhain eventually succeeds at supplanting Yggdrasil (God) and later goes on to kill her.
Hot-Blooded: Ajax embraces his savage nature, culminating in his forced evolution to Megidramon
In Harmony with Nature: Caesar, as he becomes more and more capable of accessing his reality-bending and world-altering powers.
Invocation: The Avengers and Black Hands both usually have Digivolution Chants.
Kill 'Em All: It started to turn into this by the end. It's bad to be an NPC. And bad to be a PC for that matter, Karmas, Gatmuz, Theron, Tytania and Fabian died.
One-Winged Angel: Nidhogg and Abaddon digivolve into Dexmon and Arkadimon (super ultimate), respectively during the final battle.
Shout-Out: Strom sometimes says the following phrase when lining up a long range Pendragon's Glory attack.
