The different branches have pretty different missions and that means the missions for the aircraft are pretty different. On the surface, that means the aircraft themselves are often different to accommodate that – the Army has big cargo haulers, the Navy gets short takeoff/landing and heavier gear to land on carriers, the Air Force gets long-range strategic bombers.
But that also means the chain of command should be kept internal. It’s a lot easier for the Navy to tell Navy planes what to do, following the naval chain of command than it would be for the Navy to call up the Air Force, figure out who in their chain of command can give the order for the plane they need, then ask them to issue that order, and then have that person issue the order. Of course, there’s still going to be strategic cooperation from the branches, but *tactically*, in the moment, it’s just much easier for them to coordinate within the branch.
So, for example, say the Army needs to march in and occupy a particular area. In order to do that, the need their transports to safely get there, and in order to do *that* an enemy airbase needs to be taken out and then a secure forward operating base established. The Air Force will send a strategic long range bombers to destroy the enemy air base, and in order to protect the bombers they coordinate internally to maintain air superiority. Once the base is destroyed, the Navy will move in and maintain a closer presence, securing the air space with their own fighters and using their ships to transport vital materiel. The Marines deploy from the ships to hold the beachhead, using their aircraft like Ospreys. With everything established, the Army starts rolling in with C-130s. Attack helicopters hang around to provide immediate close air support.
There are also budgetary reasons. Each branch gets its own budget from Congress and it’s easier to split up the cost of very expensive aircraft across all of the branches so they can get what they need.
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