I think that it would be very interesting to bring back Guilty Spark (either as a protagonist or antagonist depending on the circumstance). I understand that he was defeated in Halo 3, but if you read Halo Primordium it is revealed that Guilty Spark is recovered and interogated by the UNSC. At the end of the book Guilty Spark takes over the ship by overpowering the ship's AI.
Introduction: Guilty Spark could use the ship he controls to crash into the UNSC Infinity (where the Chief would be) and take it over. I was thinking this could be the thrid or fourth level in the campaign.
Use in the Storyline: According to Halo Primordium Guilty Spark's main desire is to find the Librarian. He could then state that he has found his location but needs a Reclaimer to access it. Because of Chief's skill and experience with fighting the Didact (who I presume is alive and may be looking for the Librarian himself) Guilty Spark chosses the Chief and essentially becomes his AI. It is a much different relationship though where neither of them trusts the other. For example, Chief might try to activate something that goes against Guilty Spark's agenda and Guilty Spark shuts down his armor causing him to fall to the floor, threatening to kill him if he tries it again.
Final Thoughts: This storyline would allow Chief to have an AI that is nothing like Coratana and would add to Chief's lonliness rather than help it. I was also hoping that at one point Guilty Spark could make a speech something like this, "Do you know what it's like to be turned from flesh and bone to metal. And then be forced to guard over a ring for a hundred thousand years with nothing to do. Nothing! Until finally those that should suceed me arrived. Only to have my ring destroyed, twice! But that is no matter Reclaimer. I must find the Librarian, and you will help me."
Thanks for reading and please post your thoughts.