I think everyone is confused by the Marathon/new IP stuff. This is my interpretation:
- Bungie signs the contract with Activision to make Destiny games for 10 years. They include a clause that lets a small percentage of the studio work on "Marathon" so that Bungie has something ready after it's done with Destiny. It isn't necessarily a game in the existing Marathon franchise, that's just the code name to simplify the language in the contract.
- Reach is released and Bungie is now 100% working on Destiny. (Aside from the Noble Map Pack and other Reach support before everything Halo is handed off to 343.)
- A small portion of Bungie helps with testing/producing Crimson: Steam Pirates under the Bungie Aerospace label. I'm not sure how this fits into the Activision contract, so surely there have been some additions since it was signed.
- At one point Marcus and a few other Bungie guys don't have a lot to do (or want something new) and split off to form a small team, brainstorm ideas, and make prototypes for a brand new IP. They do this under the "Marathon" clause of the contract, even though it has nothing to do with the old Marathon franchise.
- That work gets finished, shown off to the entire studio, and put on a shelf. It won't be released any time soon, but it's there for Bungie to dust off post-Destiny. The team gets reintegrated into Destiny work and Marcus retires from Bungie again. The studio is back to being 100% focused on Destiny.
I could be completely wrong though. This is just my best guess based on Twitter comments I've read - no inside info here.