These are some predictions for what happened at the end
1.The "new moon" could be the asteroid that crashed into the Gulf of Mexico 65 million years ago. The site of the asteroid impacted was where the chimera ships was hovering.
2.Recall dedealus yapping throughout the entire game to Hale about "seeing what he saw' and all that? Maybe Dedealus had some kind of future seeing ability and, if in fact, Hale got the powers dedealus had he could make Capelli "see what was coming".
3. note that Capelli had his gun aimed at Hale's head for a good 20 secs ... enough for hale to rip him to shreds with those powers...yet he didn't...perhaps he wanted to instill a huge amount of fear in Capelli before killing him?
4.In one intel it said the Chimera protected a artifact neither human nor Chimeran Is it possible that this other race the intel hints at may become a part of R3? And i think Hale is dead. I think what is likely that Capelli will become the new main character. Could the chimera actually be protecting earth from another force?
Also see the ending here,
http://www.youtube.com/watch?v=VQI_Fm48DHU&feature=related