I don't know how many people caught this particular plot point as the story of 2.0 was a bit rushed but [SPOILARZ]it's clear that Gaius was just being used as a pawn for the Ascians to activate the Ultima Weapon and it's clear he didn't realize it until it was far too late to change his mind about it. It's likely that the Ascians were going to using Ultima Weapon to absorb the power of all the Primals as their goal was to resurrect Zodiark and I guess that requires a lot of aetheric energy.
Shouldnt that have been obvious though? I mean at least it was to me when you guys got me through The Praetorium.