I just got the Game of the Year Edition of Fallout. I started MOTHERSHIP ZETA with CHARON as a follower, but he didn't join me. He's carrying a lot of my stuff and he's good backup. Will I get him back and if so, where?
You can't take any of your followers with you to the Alien vessel. Once the quest is completed you will be able to find your followers waiting for you at the place where you were abducted.
The same applies for any of the Fallout 3 DLC packs, although your followers will be dismissed from your party and be send back to the place where you originally recruited them. The exception is the broken steel DLC, in which your followers can join you.