1. Where exactly was the war room located? If it was located in raven rock, then maybe a mission tied to adams airforce base. Maybe sending the battle plan to a high ranking official stationed in the base. The point for this would be because the majority of the Enclaves vertibirds are stationed here. And they will require the vertibirds for the battle plan. (If it is a battle plan at all.)
War room is located in Ravens Rock, but we don't plan to use any BS resources in the main version of the mod.
2. Your given the mission to assassinate some important targets of the Brotherhood of Steel with a small elite unit. The targets could be caravans that are supplying the BoS, Three Dog, considering he is mocking President Eden himself and he is a main contributor to the BoS and is the Voice of the BoS. This will help Edens message to get through and help stop the support of the BoS. Other targets could be BoS Scribes.
Plausible, three dog has to be dealt with one way or another, but I don't think forcing the player to assassinate a certain target is a good idea. Maybe the PC gets to chose who to kill. Yeah, sounds good; we'll see how it goes.
3. Your mission is to deliver weapons, and ammunition to a small Enclave settlement to the east. The base is under heavy attack from BoS soldiers and is running low on ammunition. The reason it is so important is because they have captured an enemy spy, who has information on the BoS. After you bring the supplies, you are attacked again. During the attack The head Officer of the settlement gives you the order to escort the spy through the base to the other side where a vertibird is located. He gives you this order because the base will not hold out much longer and you need that spy's information. Once you get to the to the Vertibird and you are flown to raven rock were the interrigations of the spy will begin.
Also plausible, though tedious. I wouldn't mind doing it, but we'll see if Pistolero wants to create and fully navmesh another area