If any of the tools or the game are not "seeing" any of your active plugins in Mod Organizer 2, follow these basic steps to troubleshoot the issue:
1. Open Windows Explorer, go into your Mod Organizer folder, right click on ModOrganizer.exe, and click Properties. If you see an Unblock button or Unblock checkbox, Windows 10 (and possibly earlier versions of Windows) blocks UVFS because Mod Organizer is not trusted. You must click Unblock and OK to allow UVFS to work properly. You may also need to unblock all *.exe and *.dll files in the Mod Organizer folder. The easiest and recommended method is to download Mod Organizer from Nexus (or #builds on discord) to a hard drive on your PC, right click on the ZIP file you downloaded, and unblock the ZIP file before you extract the files. If you unblock the ZIP file first, none of the extracted files will be blocked by Windows. Note that if you download the ZIP file to a NAS (network attached storage) or a server on your home network, Windows may still block all extracted files because Windows treats network devices on your local network as untrusted sources.
2. Temporarily disable your AntiVirus software to determine whether it is interfering with Mod Organizer's hooking process. If it works now, add a rule to exclude the Mod Organizer folder. Some aggressive AntiVirus software prevent Mod Organizer from hooking tools and the game, and some poorly designed AntiVirus software deletes uvfs.dll without warning.
3. If this is an issue in game, disable any overlays you are using. Some overlays use their own hooking mechanism that effective disables or blocks Mod Organizer's hooking mechanism.
4. If you are running the game as an administrator but Mod Organizer is running as a regular user, the hooking mechanism will not work because Windows prohibits a process without admin rights from interacting with a process with admin rights.
5. Installing Mod Organizer into the game folder is known to cause issues with the virtual file system. It is recommended to install ModOrganizer in its own folder outside the Steam or game folders.
Thanks to ecksdee for confirming that Windows 10 does indeed prevent Mod Organizer from hooking tools and games if the executable is blocked.
I'm following the STEP guide and I've installed a few of the mods.
The problem is they aren't showing up in my load order when I launch LOOT and they're not working in game.
Iv'e been trying to look for answers for days but I can't find anything.