I just finished the whole quest and destroyed the ship, and then I saw that my items weren't returned to me. I never got all my stuff back. WTF happened?? Can someone please help out??

Your inventory items that are taken away when you are first abducted?

Your confiscated inventory items are placed in a container located in the Holding Cells area (where you first start). I don't know exactly where the container is, other than that and that it is in a small room. I believe Sally has opened the door for you. You should be able to return there and get all your items back, even though you have completed the add-on.

Yes thank god I found everything in the holding cell!! LOL