I am going to be running a new campaign over Discord with some of my friends. I've already decided that it'll be an Age of Rebellion style game, and one of the players wants to play a Spy. He and I both thought it would be a good idea if he had Secret Missions the other players don't know about. However, I am wondering how to add secret missions for him to accomplish, and also how to reward him for these missions. Since he will be doing more work, I feel he should get more of a reward, but I don't want him to get more powerful than the other players. I would appreciate any advice more experienced GMs may have! Thank you!

Duty is pretty much made for this. He has spy duties, others have other duties, and either use duty as per raw (roll each session) or give each a special mission or opportunity per mission.