Oh, and those old viral marketing Cortana messages have lots of allusions to Marathon.

I think at one point Halo was actually meant to be part of the Marathon mythos. They've obviously diverged now, but if you look at the very early Halo 1 stuff (pre-Microsoft) you can see lots of story similarities, especially with the battleroid story terminals in Marathon. Alex Seropian once infamously stated (and later retracted) that Master Chief and the Guard are the same person.

This week's podcast discussion on the Halo story made me think about just how much a shadow Halo's story is of what Bungie did with Marathon.

That's not a slight. It's just repeating a lot of the same concepts that were defined in much greater detail in Marathon, especially AI behavior patterns and Rampancy. If you have the patience for it, you'd be glad to check out http://marathon.bungie.org/story/