This has been discussed previously here.

Tldr: Third Stage is a movie.

So how do you name it so TMDB recognizes it? Do you classify it as a season or what? I have it as "Initial D (1998) - S03E01 - 040 - Third Stage" but it's recognizing it as S04E01. How does TMDB classify this movie/season?

I'm not sure what program you are using, but you should separate the TV show from the movie.

Here's an example:

/Media
   /Movies
      /Initial D: Third Stage (2001)
         Initial D: Third Stage (2001).mkv
   /TV Shows
      /Initial D (1998)
         /Season 01
             Initial D (1998) - s01e01.mkv
             ...
         /Season 02
             Initial D (1998) - s02e01.mkv
             ...
         etc.

• For Kodi check: TV shows / Movies
• For Plex check: TV shows / Movies
• For Jellyfin check: TV shows / Movies

If you're using Kodi, you can also link a Movie to the TV Show. The movie will then appear in the specials folder of the TV show.

I'm on Jellyfin, can you do anything similar or no?

I don't have experience with that platform, but a quick Google search looks like it probably doesn't at present. I found this forum discussion which might help: https://forum.jellyfin.org/t-how-to-have-mix-movies-shows-in-one-folder

Alright, thanks for the help, appreciate it. Not sure how to close or mark the thread as solved.