Flamebird and I were just hashing things out, that was a lot more detail than necessary. It's basically this:

Act 1 - Josh teaches the Fallien fighters Coronian covert tactics and Cu'Tak.
Act 2 - Josh disappears, world ends and begins again, the Fallieni stick together and survive as a group, adapting the fighting system
Act 3 - Post disaster. Josh re-emerges in the ordinary realm of Althanas and seeks out his soldiers, only to find they no longer look up to him. He tries to regain their favor with a Herculean task, fails, and it's left up to Felicity/the team to convince them to treat him as a god so he can fully ascend.

Well, act 3 got a bit complicated, but hopefully that clears it up. However you think you can fit in best will probably work.