Fire damae. Fire till she panics. You have to get rid of the shield first though.
Ok, I just looked and she just takes 20% burn damage, I think that still applies to the 5 damage that ignores armor from molotovs.
I am pretty sure I managed to panic a guildmaster that was attacking my base with fire once. It probably helped that he was the last person alive/conscious.
Sooo, do you have anything that strips armor? Chem ammo? Maybe a mind probe to look how she's faring?
Both Guildmaster and Provost have blue shields, if you manage to damage the armor enough you can attack with daze, because that ignores the shield, so you don't have to shoot that down again.
Once the shield is down you could also try the gothic raygun, or even krugers/MPGs if you have some. To bring the armor down. Just keep checking if she bleeds.
Seductress would work nicely, of course, but I take it that is not an option (yet)?
Bugeyes to panic her should work as well, if you can save her for last it shouldn't be too difficult to bring them to an adjacent room. Maybe you can control a hapless osiron guy or so as well that can try to hurt the boss or at least serve as distraction. Of course, other than that you basically bring to non combattants, what ship are you using? Can you affort two spaces for them?
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I might cheat myself a necropirate in my storage. I don't know if they can even show up in 2604, and I need one for more zombie research.
In my defence, they were introduced long after I started the game.
With gauss ammo I actually meant the craft ammo. Though I think I have plenty of the regular one as well, as I only use the sniper gauss, I prefer other weapons.
How's your radar coverage? Some ships that carry proper craft weapons usually land, depending on mission.