Since this hasn't happened before in the 100s of hours I've played Fallout 3, I'm going to figure it's mod related.
Basically, I'm not getting "abducted" like I should by Mothership Zeta. I've walked all over the space craft, played with the alien body (I even stood it up and put a party hat on it) and nothing. Is there some crazy FOOK requirement I don't know about? I have the quest, I'm where I should be, why isn't anything happening :[?
Ah... That would be my fault.
JustinOtherREF.TarAndFeather :facepalm:
The next plugin set will remedy that, but somehow the quest isn't being started by the radio transmission as 1.1 beta's plugins have it. To get the abduction to happen in the interim, just look at Recon Craft Theta for a few seconds and a GetLOS check will kick in, jump-starting DLC05MZ1. From there, make sure you grab all the ammo and alien blaster and your beam up should proceed as scheduled.
To verify this is the problem, you should get a 0 returned if you ~GetQuestRunning DLC05MZ1. If it returns a 1, then you just have to take the bait (alien tech).