In the recap of Part one at the beginning of the episode, they showed a guard standing behind Martin as Martin was doing a slime scan. However, the guard was not there in the original scene in part 1.
They knew the mothership was coming already, so why did they destroy the transmitter?
Martin, Diana and Java drive from New Mexico to Egypt in a couple of hours without the Center's assistance. How they do this in never mentioned but we have to assume Martin's watch created a portal.
Diana: Talk about not knowing someone, Billy's closet has more skeletons than a graveyard.
Martin: Oh, man. I can't believe that slimy goofball just escaped with Billy!
Java: Java no believe either. What goofball?
Diana: I'll give you a hint. If you look it up in a dictionary, you'll see a picture of Martin.
Martin: (sarcastic) Ha ha! That's so funny I forgot to laugh!
Martin: (after they are captured) Go ahead. Say "I told you so".
Diana: I TOLD YOU SO!!!!!! Oh, thanks, that feels much better now. (relieved)
(After Billy transformed into Ganthar and crashed through the metal wall)
Diana: I hope he's still on our side. (worried)
Martin: He didn't crush us. That's a good sign.
Diana: I can't believe he's gone.
M.O.M.: I can't quite wrap my noggin around it either.
Martin: It seems just like yesterday the little guy was popping up and in out of inopportune moments scaring the snot out of us on missions.
Java: Billy hero.
Billy: (popped up out of nowhere) Hey dudes.
MOM reveals that Billy was the alien from the Roswell crash years ago.
The aliens in this episode are known for stripping planets of their resources. this is a theme in many sci-fi movies, particularly Independence Day.