Hmm, not sure if you're misremembering. Marathon, a completely awesome game (I still have the original 1.4MB floppies), had two computer AIs in it. One was named Leela, the other Durandal. I'm not sure if Cortana came along with Halo, but it wasn't part of Marathon.
Microsoft bought Bungie well after the Marathon trilogy was produced, and right before they created Halo. People were bummed because Bungie had been such a Mac-centric organization, and then after being bought by Microsoft while creating Halo, they announced it would be released only for Xbox and PC, I believe.