I think you just need to read more of the basic lore, the terminal records, to figure out what's really going on. (Or just use biomatter's work on the wiki
)
You don't
have to, though, which was the point of making the lore optional while you can just focus on mechanics and reaching the surface, but if you want to make sense of some of the events and other aspects of the world, it'll take more familiarity with that background information. I'm somewhat surprised to hear you don't know what MAIN.C is yet, but I guess you're more about min-maxing for the win, which is fine, too
So the attack is the actual experiment. But Warlord says he'll lead the assault once the experiment is over. That implies the player should wait around until the assault has been defeated! The bit about joining the party could be interpreted either to help to defeat the assault as well as to join Warlord once it's over.
True, some of what he's saying towards the end could be interpreted multiple ways, though I don't want dialogue to seem too "I am NPC A and I am doing X. You can do X or Y"-ish. It's more free-form than that, but crammed into what should be a naturally flowing one-way single-time dialogue, limitations that make it harder to feel dynamic without relying on at least some ambiguity.
About the experiment, it doesn't imply that, but it's not out of the question to assume it. Why does the experiment have to finish while you're around? You're not the center of everything--in fact just a small side-player in all of what's really going on--and many of the events and encounters, especially towards the end, are meant to reflect that.
In any case, as I said earlier there will be a clearer indication that you should leave, one that I couldn't add in time for Alpha 9.