Guyver Uranus. When it reaches the point where they attempt to kill humanity by using the moon for a Colony Drop he appears to see something that disturbs him. This was because he realised that the moon itself was one of their bioweapons and it's still alive.
Appolyon is ImakarumImakarum did say that he'd go to any lengths to cure Archanfel of his slumber, and the other Zoacrystals Appolyon has been stealing were originally part of Archanfel's, so he might be able to recover by reabsorbing them.
The final battle will be Archanfel and Sho vs AgitoBecause seriously, even on a bad day Archanfel comes across more of a Well-Intentioned Extremist who views Uranus/Advent/the aliens as a threat (with a bit of revenge motivation thrown in) with several of the nicer Zoalords genuinely believing in his vision and with deep personal loyalty. Agito (and the rest of the Zoalords for that matter) are just power hungry megalomaniacs. The only thing that's keeping Sho and Agito on (nominally) the same side is the principle of 'The enemy of my enemy is my friend.' All that would take to change that situation is Archanfel (or one of the reasonable Zoalords) to convince Sho that they mean well, even if they disagree over methods.
The events take place in the same universe as PrototypeIt wouldn't be surprising if Gentek or some opportunistic American scientist managed to learn a thing or two about the bioweapons over the course of the series, and proceeded to steal samples of that for research. But in the process of synthesizing that with the Blacklight Virus, it had some interesting side-effects. Like the ability to consume bio-mass and fashion armor.
Agito now has a separate Gigantic Dark.Amniculus notes that both Guyvers equipped a Gigantic during their duel, although it's not clear to us if they were doing so separately or warring over its control again. Agito does have the Holy Coffer's control medals, so it's possible he could have had them transform into a new Gigantic offscreen, although it took Sho two years to grow his and there doesn't seem to have been that sort of time skip...