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GET YOUR LOST ITEMS BACK, SEE THIS PAGE: 
Pretty much as posted. When I started Mothership Zeta I lost all of my items, and now I'm back in the capital wasteland and still don't have any of them. Please help me get them back. Is there a console command to summon the container that has them in it?
- Well, you obviously missed the container that all of your stuff was in, and that part of the ship is locked down. So, I'd say you're screwed. Sorry. SuSpence95 (Talk) 00:06, 31 August 2009 (UTC)
i personally never had this problem (why doesn't everyone explore and open every container?) but i know you can get back to the holding cells once you're finished with MZ. now as for your belongings still being in the container, that's another story (as i never had this problem, i dont know if the stuff would still be in there)... it takes a few minutes but it is possible to get back to the container with your belongings. BraddaJ 03:10, September 2, 2009 (UTC)
I know its possible to get back down there on the PC, you just have to use some console commands but I don't know if the stuff would still be in the crate. You were supposed to get your stuff back about 5 minutes after you were released. As for the 360 and PS3 versions, I believe that SuSpence is correct, you are screwed. Unless you load a previous save.Echelon3User talk:Echelon3 05:47, September 5, 2009 (UTC)
IMPORTANT: Since it's 2011 this message is a little bit late. However, I wanted to let everyone know that I had the exact same issue. Your items are located in the steam works section of the ship which is still open. I passed my items originally because I didn't know what containers looked like on the alien ship. I spent an hour trying to figure out where they were and had to read a walkthrough to find the location. Anyhow, your stuff is safe. Just go to the matrix core through the teleporter, make a sharp u-turn and work your way back through the ship. Good luck! - Michael J. Smith - email@example.com September 9th, 2011