Tricky. It may seem obvious now to have an Air Force as a separate branch of the military, but it wasn't always so obvious. The Army Air Service was formed in 1918 and became the Army Air Corps in 1926. The Army Air Corps became the Army Air Forces in 1941, and was split off into its own branch of the military in 1947.
Basically, the role of the air units in the army became more and more separate form the role of the ground units, and eventually, it was decided that it would be better to have them as seperate branches, but it didn't have to be that way. It's your choice what to split off, I think it makes the most sense when the roles become so disparate that they have little in common.
For example, if you have time travel stories, the organization dealing with time travel might work best as a separate branch. Planetary defense might become very distinct from a deep space patrol service.