Guyver/WMG

The moon is alive
In Chapter 173 Agito begins to view the records of 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.
 * As an extension of this theory, Appolyon is from the moon, kept as an emergency plan which was only activated recently, possibly due to the activation of the first Relic.
 * This, obviously, means that Sho will eventually fly to the moon and turn it into another suit of armour for the Gigantic.
 * Um, guys? That wasn't the moon. It was a random planetoid hucked at Earth. Archanfel smashed it to rubble, some of which impacted with only enough force to start an Ice Age. The thing that disturbs Agito is probably the revelation that Archanfel is just that powerful.

Appolyon is Imakarum
Imakarum 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 Agito
Because 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 Prototype
It 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.
 * It'd be an interesting cross-over to say the least. Hell, they should at least make the armored form for the sequel have an alternate look that looks more like the guyver