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I downloaded some necessary mods from Nexus using MO2 (Mod Organizer 2) and SKSE64 20019 from Silverlock. My Skyrim SE version is 1.5.97 SKSE is installed properly, I know how to do it. So here's the problem, I used the MO2 in admin mode and tried to launch SKSE via its loader with Steam running in the background but it crashes after command.

When I start Fallout from Mod Organizer 2, the loading screen shows for 1s then the game crashes. This happens both when I start F4SE or the original exe from mod organizer. Both F4SE and Exe start correct when I start them outside Mod Organizer. Moreover, I reinstalled Mod Organizer 2, set up all my mods, copied in a last save game.
SKSE and Skyrim SE (properly and completely cleaned with SSEEdit) crash to desktop with no errors when launched from Mod Organizer 2. This always happens with or without mods. Resetting Skyrim SE's settings does not help. Both SKSE and Skyrim SE launch with no issue if not launched from Mod Organizer 2.
Simply unpack Mod Organizer wherever you want and run it. On first startup Mod Organizer will ask you which game to manage unless you placed it inside a game directory. Compatibility The Mod Organizer works with almost any tool I've tried so far. What this means is that they can be made to work on the 'virtual' data tree.
This mod seems to have been causing crashes in most but not all cells, as I was able to load new games with Alternate Start LaL, but then when I left the starting cell the game would crash. I have no idea why this mod suddenly started causing my game to crash, but I hope this is helpful to anyone experiencing similar issues. The general method.

1Internal Mechanics
- 1.3Virtualized Files
2Maintenance
- 2.5Optimal Install Locations
5Migrating Other Mod Managers

< Guide:Mod Organizer

Mod Organizer Advanced/Technical Guide -- by DoubleYou & the STEP Team

GUIDE FORUM THREAD
OFFICIAL SUPPORT FORUM

Internal Mechanics

The Virtual Filing System (VFS)

As explained in the FAQ, Mod Organizer (MO) uses mod isolation, a feature in which every mod is installed into its own directory. This provides for an untouched game data folder, void of installed mods, which is the main feature of MO. This section will not only discuss the technical details and challenges of this approach, but also its advantages and disadvantages.

It will be discussed for Skyrim but is valid for all four supported games. When Skyrim is installed it stores all its files on the file system (FS) of a disk. The same is true when you install the official DLC's. The behavior of Skyrim can be changed by installing mods and plugins.

Note: Mod managers like Nexus Mod Manager (NMM), Wrye Bash (WB) and Mod Organizer (MO) can only install files in the <Skyrim>/data directory. Hence plugins like ENB and SKSE cannot be installed by them.

Typical mod managers like NMM and WB install mods into the data directory of the game being modded. When installing mods, they keep a record of all installed files. This allows them to detect if a mod overwrites files of the original game and/or one or more existing mods. The user is given the option to overwrite such files. All files are added to the original game data directory. Hence the once empty and pristine state of the game data directory is lost. These programs have algorithms to restore files on the FS when, for example, mod B, which had overwritten files from mod A, is uninstalled. When using Profiles and changing the order in which mods were installed, these programs make changes to the windows file system by copying/deleting files on it. Depending on the performed actions this can take considerable time. If these programs work perfectly and Windows works perfectly, no harm will be done to the file system and the game continues to work. Unfortunately, this is not always the case, and problems may arise.

Mod Organizer takes a very different and revolutionary approach. It never writes files to the game data directory, but instead creates and uses a virtual filing system (VFS). It is called virtual because it does NOT exist on the regular file system and only exists when MO tells a program it exists. When the game is started by MO, it is unaware of this VFS and thinks it uses the regular Windows file system. Therefore, all installed mods are loaded and used normally. The same is true for any other program started by MO (e.g., BOSS, Boss Userlist Manager (BUM), WB, etc.).

The VFS is constructed using a technique called hooking. Hooking is not an uncommon technique and progams like SKSE, ENB, SweetFX and ENBBoost use it. In the case of MO, hooking involves intercepting the Windows system calls and injects its VFS into the file system. In other words, it 'hooks' itself into the regular Windows filing system and changes it. The hooking is performed by a dynamic link library (DLL) created by Tannin, a part of the MO program rightly called hook.dll. Other open source hook libraries exist, like EasyHook. Users interested in the technical details of 'hooking' are encouraged to read the section 'EasyHook and 64-bit support' below.

The VFS is constructed from the following:

The regular <Skyrim/Data> directory and all its subdirectories.
The <MO>/mods directory
The <MO>/overwrite directory.

The section 'Files and directories which are virtualised' gives a complete list of what is virtualised. The above shows in which order the VFS is constructed and what overrides each other.

Regular <Skyrim/Data> directory.
This is the base and nothing needs to be added or injected.

The <MO>/mods directory.
In MO a mod is a directory in the <MO>/mods directory. All files in each directory are injected into the VFS. The order in which files are overwritten in the virtual data directory is explained in the Priorities tab of the wiki.

The <MO>/overwrite directory.
The last files injected into the VFS are the files in the <MO>/overwrite directory. But what is this overwrite directory? Basically and simplified it contains files which are created by a mod or plugin after its installation. Examples of this are files generated by Skyproc-based programs programs such as Automatic Variants (AV), a 'Bashed patch.esp' created by WB, and log files generated by skse based mods like Elys meminfo.

IMPORTANT. MO does not know about the relationship between files in the overwrite directory and the mod which generated it. Hence it does NOT obey the priorities set for a mod in the left pane. Which means you always have to make sure the overwrite directory is empty. The overwrite directory is global for all profiles. Some users have expressed this to be a drawback. For more information about the overwrite directory and strategies how to simulate a 'local overwrite for each profile' can be found in the Overwrite tab of the wiki.

Advantages of the MO VFS approach

Speed. Changing the install order mods is instantaneous because no files have to be copied.
An untouched Skyrim/data directory, because it does not change any files on the file system for the supported games (with few exceptions).
Manipulating mods and the overwrite directory can be done using the default Windows Explorer.
Mods can be installed outside of MO, since a mod is nothing more then a directory inside the <MO>/mods directory.

Disadvantages of the MO VFS approach

The overwrite mechanism is confusing as it can't be made consistent for all mods/plugins.
There is no 'local overwrite' directory for each profile.
No support for 64-bit programs.
The hook mechanism is the Achilles' heel of MO and fragile.
The hook mechanism doe

Mod Organizer 2 Crash On Startup