: Infiltrates Covie bases, Innie Bases, UNSC INNIE Sympathizer
: homes...Assassination missions, intel gathering.

I would change the protagonist from a simple, loyal ONI agent to one with curious or even serious sympathies for Insurrectionist movements. The sort of lengths that these individuals would go to in walking the fine line between serving the country and protecting their people would be excellent to witness. It might not come down to good/bad gameplay choices like Mass Effect, but it would make you think if betraying or killing your comrades is justified compared to the bigger picture of independence.