Were all our efforts wasted? *spoilers*

[Mudd]

In the storyline Gaius Van Baelsar was already plotting his agenda against Nael Van Darnus because he saw that Nael had become deranged. In the flashback with the soldier dying, at least for adder company, Gaius is having second doubts about Nael's plan, because as he states "What good is conquering the world that is destroyed?"

Maybe the reason Gaius was on the airship was he was leading a fleet of his own, knowing Bahamut was inevitable at that time, and going to try to repel him from destroying everything totally.
Maybe Gaius Van Baelsar has gone rogue and is trying to right his wrong of letting Nael plot such a catastrophic event.

That'd be neat