Good ideas there Temis. I agree that there is enough stuff there for a good story even without my macguffin(I had to look that up Hahaha). And for those in the B and C plot that pretty much what the story would be. Only those characters in the A plot know about the true motivations behind the war. The A plot centers on this device the "eye of Senak" It speaks of it's creation and uses. The A plot tells of Senak gathering forces on Romulus and then attacking Vulcanis(or Vulcan if you prefer). He is eventually defeated and retreats to Romulus. Becuase of the "Eye" he is immortal so to speak and begins re building his troops to try again and conquer Vulcanis. The "Eye" ends up in the hands of the humans. So Senak's motivation is primarily revenge. However Senak is not seen by most Romulans. He is more like a sit-in-a-big-throne-and-command guy. Physicaly weak but very powerful. The reason I decided to put the A plot in my story is to give it a more epic almost mythical(or dare I say fantasy) type feeling. So the A plot is more of the secret society "we know what's really going on" plot. I don't like the idea of S31 much earlier than DS9 where it was mentioned. Earth has come out of WWIII and in some ways still recovering. Humans are toward the end of becoming "advanced." I'd hate to think we'd still have secret government organizations working behind the scenes. The United Earth government is fairly new and I imagine because of WWIII the founders made sure to pass laws to prevent the formation of such secret societies.
The B plot which focuses on the Crew members of the Enterprise (except Captain Stiles because he is tied up in plot A). It is about their missions during the war. Since the Captain would not be aboard we would mostly see the first officer in command of the Enterprise. But I don't want to make it seem like the Enterprise is the biggest most important ship in the fleet, it's not. It's just another science ship that got dragged into the war.
The C plot would be the rest of the war effort. This wont neccessarily be the main plot but will probably be the biggest. The B and C plots will intertwine pretty often. The C plot would focus not only on earth ships but allied ships. I want to include ground battles as well as space ship battles. I want ground battles to give it a bit more of a Halo feel, with ground vehicles and tanks, and whatever other alien equipment there would be. The ground battles would be fought be by a division of UESPA called the Special Space Task Force(SSTF). I guess it could be called like a "marines" or something but I hate putting Marines on space ships. The SSTF would use United Earth Army ranks but would also include pilots, and naval vehicles.
I added the SSTF for two reasons. It seemed more reasonable than putting UESPA on the ground. Also it explains part of the experpt from Picards scrapbook about "Federation Day." It mentions Georges Picard and that he is a Major General of UESPA. Since UESPA has naval rating having an "Army" branch of UESPA helps explain it.
I also want to include another species of allies or maybe Romulan allies. They would be the Greys. You know big heads, small bodies, big eyes, flying saucers all that stuff. But I would also explain why we never see them in later series'. I like the idea of them having conflicts with the Vulcanians. Sort of taking the place of the Andorians in ENT.
The conflicts could come from the two species approach to exploration. Vulcanians: Watch, take notes, don't interfere. Greys: Go down, abduct specimens, take samples, maybe even enter into alliances with governments to trade technology for genetic material. The whole Grey thing needs some work but I like it.
Sorry I went on so long. I didn't mean to write so much. I just started throwing my ideas out there for my book series(which would never get published because of copyright laws).