... equip the three folks you are planning on using again with all the gear, base mods, and ammo (and at least one gas can between them) you can load them up with, even if it encumbers them before you do the last leader mission.
Unlike when you run the first game on endless, your shit doesn't transfer here, and once you complete that final mission, the game isn't kidding about not being able to access that base ever again. You can't even switch characters from your leader. So, if that person isn't one of the three, you're totally hosed.
You lose everything you saved up in the box on the restart. I had a LOT of good guns and ammo that got wiped.