The story starts out with the man guy and he can talk to animals, he ends up finding an injured cat only it turns out that the cat is a yokai. So he helps the cat heal but it leaves too soon and its not fully healed, so the main character runs after him. The cat is confronted by another spirit and the spirit attaks. The main character shows up, tries to help but ends up dying, so the cat decides to merge with the main character. I also remember the main character was raised by his grandfather, there was a secret government organization, which the grandfather was a part of in the past. Can anyone help me out?

I think youre talking about Black Torch.

https://www.mangaupdates.com/series.html?id=138753

Yes!!! That’s exactly it! Thank you!!