I ran out of money in-game, didn't realise you could sell some of the stuff you extracted. I thought them guns and mortars were going to be used as weapons on the base, so very quickly solved the money issues. Happened to go back to Motherbase when the moral was low, so witnessed a fight between comrades.
Like @Hero\-of\-Time, i tranq'd most of the enemies and extracted back to base. But for a while now, i've been sending back the highly skilled troops to base. I'm trying to get the resources saved to get a sniper with a silencer.