mod organizer Crash to Desktop when launching Skyrim SE through Mod Organizer 2

[CayugaDuck]

I am having a strange crash-to-desktop error when trying to boot skyrim through MO2. Whether I try and run the game through skse_64 or the regular launcher through MO2, the game boots until the Bethesda logo, then crashes to desktop before the main menu.

The same error occurs when I tried to make a new instance with no mods, both for skse launcher and the regular skyrim launcher through MO2.

The game is able to successfully boot to the main menu if I launch the game from steam (and I am able to start a new game fine), or directly run the skse_64 exe from my files. 

Another strange quirk is that other applications like FNIS and LOOT crash when I attempt to run their functionality. FNIS crashes when I click “generate” and LOOT crashes when I try to sort the load order.  

I tried to see if it was a strict MO2 issue by seeing if my modded FO4 would run, which it did perfectly. Other than the inability to fully boot Skyrim, I cannot tell if there are any other issues with my mods or load order or anything as the crash doesn’t return any error message.

I have tried reinstalling SKSE, I updated MO2 to the latest version, and completely uninstalled and reinstalled Skyrim, to no avail. My game was working fine last I played in late September, since then I haven’t touched anything. All I have done was set my skyrim steam appmanifest file to read only to avoid updates, which hasn’t been a problem on the past. I am truly lost as to what the issue could be.

If you require additional information from me, I’d be happy to provide. 

[CayugaDuck]

  On 3/29/2025 at 1:55 AM, GSDFan said:

I typically only use manually installed, portable instances of my MO2 installs, so my previous comment reflected that instance. Global instances will reflect the "C:/Users/UserName/AppData/Local..." path as a base directory. 

I noticed in the second set if screen shots the Managed game points to "D:\SteamLibramy\steamapps\common\Skyrim Special Edition\SkyrimSE.exe". I think that it should just be the path to the folder, "D:\SteamLibramy\steamapps\common\Skyrim Special Edition". That is probably where the problem is.

 

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That's weird, because my Fallout 4 paths for "Managed Game" also ends with the game application, "Fallout4.exe" and works fine. How would I set it to just the folder directory? It seems to only allow me to select an application or file rather than a folder by itself.

[CayugaDuck]

  On 3/29/2025 at 3:08 AM, z929669 said:

Apologies, I should have read the OP more carefully.

Defaults in instanced for me, and it works without issue.

 

Assuming that when "uninstalled and reinstalled Skyrim", the game directory is totally clean of any third-party binaries and the like. Since this is specific to SSE/MO and other games run fine though MO, it has to be something associated with the SSE MO profile, SSE itself, or the SSE registry settings. Running via the Steam Launcher should properly set the registry. It might be a good idea to verify the game files via Steam and re-launch via Steam just to satisfy any lingering OCD.

The only thing in the posted MO log I see that stands out is that there is no profile set, so it's reverting to default. Maybe set a profile, and tick all three boxes for profile specific * and auto archive invalidation. This is a shot in the dark.

Can MO be configured to produce a more verbose log?

I would also examine files under \Documents\My Games\Skyrim Special Edition.

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Upon my first troubleshoots before/after reinstalling I ran the game through steam (which loaded fine, as well as loading a new game without issue), as well as verified the integrity of the game files. The issue persisted. I will admit I am not very savvy when it comes to advanced MO2/SkyrimSE settings, so I would be unaware of any leftover binaries or what that would involve.

I'm not sure what setting a profile and enabling the profile specific saves/INI files would entail, or if it would mess with my current save games or game data. Again, I checked my modded FO4 instance, which loads fine, and it too uses a default profile. The only difference is that us uses profile-specific INI files. My usual Skyrim playthroughs that have been encountering the CTD problems also have the profile-specific INI files option selected.

Is there anything out of the ordinary I should be looking for in \Documents\My Games\Skyrim Special Edition? Here's what the base directory looks like: 

[GSDFan]

  On 3/29/2025 at 3:37 AM, CayugaDuck said:

That's weird, because my Fallout 4 paths for "Managed Game" also ends with the game application, "Fallout4.exe" and works fine. How would I set it to just the folder directory? It seems to only allow me to select an application or file rather than a folder by itself.

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Sorry, Bad info. I not sure why mine didn't have the .exe, but now when I check they have the full path to the executable. Again sorry.

[GSDFan]

The only other thing I can think of is to make a new profile from the profiles manager. Select Create and when the window opens give it a name and check the box to the left of the Default Game INI Settings check box. At least this will eliminate your configuration files as being suspect.

[CayugaDuck]

  On 3/29/2025 at 4:55 AM, GSDFan said:

The only other thing I can think of is to make a new profile from the profiles manager. Select Create and when the window opens give it a name and check the box to the left of the Default Game INI Settings check box. At least this will eliminate your configuration files as being suspect.

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Did this, still had the CTD. So I guess it's not the configuration files?

[GSDFan]

  On 2/21/2025 at 5:26 PM, CayugaDuck said:

Another strange quirk is that other applications like FNIS and LOOT crash when I attempt to run their functionality. FNIS crashes when I click “generate” and LOOT crashes when I try to sort the load order.

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In MO2 executable drop down there is a bundled file explorer, can you run this? It should open to the Data folder. You can change the view to details for easier viewing. Open the game directory and see if it looks like this:

You can also run any executable from here. So if the file explorer did run and open then MO2 has used the virtual file system successfully, thus eliminating the core of MO2 as a problem. Try running in this order the launcher (SkyrimSELauncher.exe), the game from the launcher, the game (SkyrimSE.exe) and then skse64_loader.exe. Post your results.

  On 3/29/2025 at 3:08 AM, z929669 said:

Maybe set a profile, and tick all three boxes for profile specific * and auto archive invalidation. This is a shot in the dark.

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At least in my setup Mod Organizer disables archive invalidation.

[CayugaDuck]

  On 3/29/2025 at 6:43 PM, GSDFan said:

In MO2 executable drop down there is a bundled file explorer, can you run this? It should open to the Data folder. You can change the view to details for easier viewing. Open the game directory and see if it looks like this:

You can also run any executable from here. So if the file explorer did run and open then MO2 has used the virtual file system successfully, thus eliminating the core of MO2 as a problem. Try running in this order the launcher (SkyrimSELauncher.exe), the game from the launcher, the game (SkyrimSE.exe) and then skse64_loader.exe. Post your results.

At least in my setup Mod Organizer disables archive invalidation.

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Here is what my D:\SteamLibrary\steamapps\common\Skyrim Special Edition path looks like, as well as the D:\SteamLibrary\steamapps\common\Skyrim Special Edition\Data looks like:

Something I notice immediately is a Veeam vdf file (A file backup software) in my Skyrim Special Edition folder back from February 13th, which is the same day I started to have the CTD issues. But what makes that confusing is that the same file is in my Fallout 4 folder, a game which boots totally fine, so I don't see how that's the issue. If there is anything else that seems out of the ordinary, please let me know. 

I tried running all three executables, SkyrimSELauncher.exe, SkyrimSE.exe, and skse64_loader.exe directly from the file explorer in the order you specified, and all three still have the same CTD issue upon booting.

I also created another un-modded test instance with archive invalidation disabled, profile specific INIs, and it changed nothing. Same CTD. I will note that upon creating all these new instances, this pop-up appears and I've just been pressing "Do Nothing" for all of them. Again, I don't see how this could be the issue because all my gameplay instances were running fine long before the CTD issues and this doesn't seem to change anything. 

I think the FNIS and Loot errors are notable in that they indicate there is some problem with MO2 reading or writing Skyrim SE files. I can't think of why or what would be causing that. I did set the Skyrim appmanifest file to "Read Only" such that my game would not automatically update, but I did that long before the current CTD issues. I have also set my Fallout 4 appmanifest to "Read Only" and the game works fine through MO2. That's really the only thing I can think of, otherwise I am really at a loss. 

[CayugaDuck]

  On 3/29/2025 at 11:10 PM, GSDFan said:

I was doing some reading of issues on the Mod Organizer github and stumbled onto an issue the same as yours, crashing when launching applications through MO2. A couple of users there stated there they were using BitDefender Antivirus. They also stated that they were also using BitDefenders Advanced Threat Defense which is separate from the AV.

It looks like one of the users outright disabled the threat defense and the other made some exceptions to the advanced threat defense.

I took the liberty to copy them here in case you also use that.

• (MO2 Install Directory)\modorganizer.exe
• (MO2 Install Directory)\ufvfsZ_Zproxy_x64.ext
• (Skyrim special edition Install Directory)\skse64_loader.exe
• (Skyrim special edition Install Directory)\skyrimse.exe

 

From <https://github.com/ModOrganizer2/modorganizer/issues/1808>

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Yes, I do use Bitdefender and I was unaware of the Advanced Threat Defense feature. I did as you suggested, adding the provided files to the exception list, and the CTD error continued. BUT, by disabling it completely, my game was able to boot properly! Even was able to load into a save, everything loaded no problem. Tried it with my un-modded instance, as well as my regular gameplay instances. With the Advanced Threat Defense disabled, the game is able to boot, as well as LOOT, FNIS, and Nemesis.

Very frustrating! There were no errors or any indication that Bitdefender was interfering with my files like that. Ideally I would like to figure out exactly what it is blocking so I don't need to keep the AVD off entirely, but I am just happy we have seemed to determine what the problem is. If you have any suggestions to what other files or directories I can add to the exception list, please let me know. I really do appreciate all the assistance you have given me. Thank you very much!

 

Edit: Tried adding my base Skyrim Special Edition and Mod Organizer 2 file directories themselves to the exception list, and it was still having the CTD issues, so it seems that keeping it off completely is the only fix as of right now.

Edited March 30 by CayugaDuck

[z929669]

  On 3/29/2025 at 11:10 PM, GSDFan said:

I was doing some reading of issues on the Mod Organizer github and stumbled onto an issue the same as yours, crashing when launching applications through MO2. A couple of users there stated there they were using BitDefender Antivirus. They also stated that they were also using BitDefenders Advanced Threat Defense which is separate from the AV.

It looks like one of the users outright disabled the threat defense and the other made some exceptions to the advanced threat defense.

I took the liberty to copy them here in case you also use that.

• (MO2 Install Directory)\modorganizer.exe
• (MO2 Install Directory)\ufvfsZ_Zproxy_x64.ext
• (Skyrim special edition Install Directory)\skse64_loader.exe
• (Skyrim special edition Install Directory)\skyrimse.exe

 

From <https://github.com/ModOrganizer2/modorganizer/issues/1808>

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Nice find.

  On 3/30/2025 at 12:52 AM, CayugaDuck said:

Yes, I do use Bitdefender and I was unaware of the Advanced Threat Defense feature. I did as you suggested, adding the provided files to the exception list, and the CTD error continued. BUT, by disabling it completely, my game was able to boot properly! Even was able to load into a save, everything loaded no problem. Tried it with my un-modded instance, as well as my regular gameplay instances. With the Advanced Threat Defense disabled, the game is able to boot, as well as LOOT, FNIS, and Nemesis.

Very frustrating! There were no errors or any indication that Bitdefender was interfering with my files like that. Ideally I would like to figure out exactly what it is blocking so I don't need to keep the AVD off entirely, but I am just happy we have seemed to determine what the problem is. If you have any suggestions to what other files or directories I can add to the exception list, please let me know. I really do appreciate all the assistance you have given me. Thank you very much!

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In case you consider BitDefender alternatives, I use ESET AV. It has no such issues and is quite reliable in terms of threat protection.

[CayugaDuck]

  On 3/30/2025 at 1:07 AM, z929669 said:

Nice find.

In case you consider BitDefender alternatives, I use ESET AV. It has no such issues and is quite reliable in terms of threat protection.

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Yeah, I used ESET before in the past but it was part of a work license, so I do not have access to it anymore. I will corroborate that I had no issues back when I had ESET. Just glad this seems to be the fix we were looking for. 

[GSDFan]

Good to hear. A quick AI search gave me this link, Threat logging on Bitdefender support center. It looks like there is a log page that might shed light onto what it was blocking.