Despite doing everything possible to try and progress the quest (literally every option was explored, as according to the strategy guide), I had to complete it in the most unsatisfactory manner. I'm neutral with the Khans, by the way.

The problems:

Melissa not showing up at the camp, despite there not being any reason for her not to be there.
Colonel Moore dialogue not updating.
Papa dialogue not updating.
Female chemist (I forget her name - one of he advisors) wants proof, but doing what she requires doesn't update her part of the quest.

I figure what has happened is that because I decided to do a lot of exploring before tackling the main quest line, maybe my earlier interactions (the majority of which are only partaking in conversation) with a few of the quest NPCs threw everything into chaos. If that's the case, it kinda goes against the whole point of having an open world environment.

Lucky for you, for what i have read, the following Patch should fix this bug. It should come up this week, maybe today.