A: They're aliens in disguise slowly trying to take over the world with control (why would they hide area 51 if they weren't aliens? Its' their landing site!).
Q: If adults go to work, and kids go to school, where do babys go?
I heard they are making the second metroid prime more 3rd person. Thats a bad idea, its cooler, and more fun in 1st person, unless your morph balling and using cutscenes.