Well, I see Melkor as a new, young recruit who is propably pretty nervous about his first mission, but on the other hand he has certain doubts about Zion as mostly military organization- he always desired freedom most of all, and following orders he doesn`t understand doesn`t make him that happy. But he despises Matrix much more, so is quite willing to obey his superiors.
I assume a part of the crew could be ordered to remain as backup?
Surveillance duty has become a popular excuse for why people aren't present in a mission, when it comes to absentees and new players. I use it for writing up Mors' story.
Always gotta watch for those Sentinels...?
I dunno.
Anyways, I'm guessing shotguns would have been more like it against those Vamps in terms of dealing killing blows? Maybe?
As for factions...
The Werewolves and Vamps were in league, the Merovingian's faction.
Then the SWAT, which we assume might have had something to do with Melitus.
Then the Hunter on his own, whatever he was up to.
Then the Doctor. He went straight for the Hunter...curious, that. Spike, Lana, and I chatted about it, we supposed that maybe, since the Hunter is a program error, the Doctor is the "cure" for the problem, like Agents to humans. Could be more personal, but I assume he wasn't in league with anyone there.
Then the Maintenance men that the Werewolves got the box from.
Then us!
Six factions total, unless there are more alliances there. Of the six factions, the Hunter and the Maintenance Men were there for the Key. The Werewolves wanted the box. The Doctor wanted the Hunter? I have no idea about the SWAT, they just kinda showed up and started shooting. Probably wanted the key as well. We wanted to find out what Exiles were, and we somehow ended up with a Key too.
Ah well, Melkor there is asking questions that get to an area that Dexx had issueds with last time, Must be an East European thing.
Zion is generally aware that programmes are intelligent. Humans created the first truly sentient AI, after all.
As for non-system AIs, that is not generally known, no, although the most accepted theory about the Oracle is that she, surwly, is a programme too.
You people playing this mission are a little different, Some of you actively met such things last time, the rest have been told they exist, though meeting such strangeness in the Matrix might well be a shock.
Are they really alive? Ultimately, no-one can answer that question even for other Humans. By all observable and measurable means, full AIs like The Oracle, Agents, and those Werewolves, are as alive and sentient as any Human, but with a non-Human mindset, almost like an alien race.
Contrast Melitus' goons from the last game, who Melitus himself specified were not sentient, were basically automatons, less alive than even a plant. Inside the Matrix, where there is no biology and all is code, his masked servants may as well have been walking tables with a speech box attched.
What you believe about all this is up to you, but the basically presented scenario assumes they are fully realised sentient beings, but most Humans also assume they are evil, or at least against Humanity for those who reject concepts like evil.
The broad thrust of your mission is to find out if such things are a security threat, and so you are taking an aggressive stance by default. Could there be allies to be made? It seems unlikely, but then you are back to using the Oracle as an example again. The films- through The Oracle, Seraph and some other touches- certainly presents the idea as feasiblr.
Yes, the Philo Path does not explore all issues at once, that would be rather... well, bad in many ways.
What makes a being a being was very much the focus last time, with all participants met with identical duplicates of themselves and asked to choose which one would walk out alive. And so hence one of the big things explored n the preamble to that was the concept of self, sentience, and even soul, in order to discern what each player believed so that his final choice could be seen in cntext.
You may wish to remember that all Exiles draw power from the Matrix also.