For example
With the Institute, you'll have the mass fusion tower battle with the BoS and the epic battle where you invade the BoS airport.
With the BoS, you'll have the mass fusion tower battle, the battle where you escort prime to the C.I.T building and finally invading the institute itself.
With the Railroad, you have to fight off the BoS invaders in the Railroad HQ, invading the BoS police station, the battle on the BoS airship, and finally the institute HQ.
With the minutemen, you get to defend your HQ from the institute, invade the Institute HQ and finally defend the castle from the BoS if you want to.
I didn't count bunker hills because bunker hills.