[Chojin]

Everything I put up there is also from Bungie themselves. If Halo no longer has anything to do with Marathon, it's something they decided after they made the game. The guy in charge of Cortana (and a good deal of Marathon's storytelling, as their creative director) left shortly before Halo came out.

Most likely Halo was meant to be a prequel and staged that way, but after Nathan left they decided to use what he had and ran with it in a different direction.