So, I just finished the game. As many of the reviews said the story is a tad confusing although I've structured what I think overall what was going on at least at the most obvious level.
Seems to me David's whole intention from the beginning was to essentially anoint Mondo "ruler of the moon" you could clearly see Mondo absorb a small amount of Dark Moon energy every time he killed one of the bosses. Slowly corrupting him.
I'm also assuming David had Dolly (I think that is her name?) try to obfuscate Mondo's true memories so he could be more easily manipulated. Even knowing the secret Mondo still didn't put two and two together until it was too late and he was corrupted. Still not sure what is going on with Mika and David I was thinking Mika was insinuating that she was actually a wire. Not sure. Although I don't see that being the case as wires are all hallow emotionless shells.
I also just replayed the 2nd Mission again and you can clearly hear Liam O'Brien a.k.a David's voice telling Mondo to "Wake up" and then at the end of the mission you can hear him say "Let the Killing begin" not sure if this implies that David was inside of Mondo's head from the beginning or what.
I'm interested to see other people's interpretations and deconstructions of the plot because while sort of obfuscated I think there is probably something interesting to this game underneath the surface.
So anyone have any other ideas about what is going on?