Red Wood was a crafts pony from a small village, but his simple life came to a sudden end when he died....but he got better...but with a new tenant sharing his body with him. An alien from a different world, sent here as a trail blazer. The Alien left his body behind and needs to share Red Wood's.
This would have been complex enough, but there was an old evil cult that knew about the alien and wanted his knowledge and science for themselves. And to at least one critical sense, they got what they wanted, a way to use the Alien mind uploading technology to rapidly take over the minds of innocent ponies, when they're must vulnerable during acts of intimacy, forced or not.

Now its a war where ponies on both sides are former friends and allies.

(Note: Marked 'Sex' due to frank mature events, but not a Clop fic, and marked 'Gore' but violent scenes are infrequent and quick)