I read an idea a long while back that I'll repeat:

A spy game in the style of Splinter Cell, except you aren't the guy, you're his handler. You tell him "crawl under that laser," or "wait a moment, there's a guard... okay now go!" or "input the following sequence to disable the doomsday device," and he more or less listens to what you tell him to do. The issue is that the more you fuck up and get him hurt or killed, the less likely he is to listen to you. So you have to build up a relationship with your spy by giving him good instructions in a timely fashion and getting him to complete missions successfully. Over the course of the game, as you progress, you'd be able to tell him to do more dangerous things because he'd trust you more. Playing the game successfully would make you feel like you and your spy were a well-oiled machine, working together to take down supervillains and criminal syndicates.