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Mod Manager

This guide was written specifically for use with Mod Organizer 2 and it's in-built functionality. Any attempts to use alternative mod management systems are unsupported. Some users have had success doing so, but any support will be unofficial and from other users only.

The paid-version of ccleaner is known to have conflicts with the Virtual Filing System (VFS) used by Mod Organizer 2. Unchecking the 'Windows Event Logs' option under ccleaner's advanced tab will help prevent this incompatibility.

Mod Organizer 2

Mod Organizer 2 - v2.2.0 - by Tannin

Files to download:

  • MAIN FILES - Mod Organizer 2 (Archive)
  • Download the linked file above.

Special Instructions:

WARNING: Mod Organizer 2 MUST be installed in portable mode. The Script ReLinker functionality of zEdit requires this management method to complete it's work. This are no workarounds for this requirement.
  • For the more visually oriented, the guide suggests watching this to help you become familiarized with the install procedure. Skip to 10:27 for the relevant portion.
  • Install Mod Organizer 2 by:
1. In the root directory of the drive where you have installed Skyrim, create a new folder. It can be called anything you wish, but should be easily recognizable to you. It will appear something on the lines of E:/Mod Organizer 2 - Lexys LOTD SE.
2. Extract the contents of the file downloaded above to the folder you just created.
3. Run Mod Organizer 2. If you desire, you can also create a desktop shortcut for MO2 at this time, as you will likely be using this program quite a bit.
4. In the pop-up that appears, you will be prompted to "Choose an Instance". Select Portable.
5. In the next pop-up that appears, select Skyrim Special Edition from the drop-down menu.
6. A third pop-up will appear, asking if you want a tutorial on the tool's use. Those who have never used any version of Mod Organizer (including MO1) should select Yes for a quick run-down on the features of the program. All others can select No.
7. A fourth pop-up will appear with the notice Mod Organizer is not set up to handle NXM links. Associate it with NXM links? This is recommended to be set to Yes, as this will allow MO2 to handle all downloads possible from the NEXUS file links.


  • Ensure that you do not move the mods folder out of MO2's install folder at any time. This is needed to ensure that MO2 can see the mods you are about to install.
  • Similarly, do not move the profiles folder out of MO2's install folder at any time. This is needed to ensure that the Script ReLinker functionality of zEdit works as intended.

Configuring Mod Organizer 2

With Mod Organizer 2 now properly installed, there are additional settings that will be required to ensure full integration with the NEXUS and user comfort.

Special Instructions:

  • Mod Organizer needs to be connected to the NEXUS for account logins and download management.
1. Full integration with the NEXUS requires that you have a NEXUS account. If you do not have one, you can create one here. This will also be required for large file downloads, and is free of charge (though a free account will also be very limited in bandwidth). Premium account, with no bandwidth cap, are availible. Details can be found on the NEXUS website.
2. In the toolbar of Mod Organizer 2, locate the 'Settings' button (it will have a spanner and screwdriver icon on it... wrench and screwdriver for you Americans).
3. At the top of the window that appears, press on the Nexus tab.
4. Click on the Connect to Nexus button.
5. A new window will open in your browser, and the Nexus will request permission to link Mod Organizer 2 with your Nexus Account. After allowing this, you can close the browser window.
6. In the Mod Organizer 2 settings menu, press OK.
  • Some users may find the default MO2 theme overly bright or harsh.
1. In the toolbar of Mod Organizer 2, locate the 'Settings' button (it will have a spanner and screwdriver icon on it... wrench and screwdriver for you Americans).
2. At the top of the window that appears, press on the Geneal tab (if not already selected).
3. In the upper right corner of the Settings window, locate the Theme dropdown (possibly with the word "None" in it currently). Any theme may be selected, based on user preference. Most users report the most comfort with the 'dark' or 'Paper Dark' themes.
4. After selecting a theme, press OK to close the window.
5. In the pop-up window that appears, allow Mod Organizer 2 to restart to apply the theme change.

Depending on your specific download practices, the downloads for the mods can well over 100 Gb of data. If you have installed MO2 onto a relatively small drive (such as a small SSD), you should consider changing the location of MO2's download storage to a larger location. This can be done by creating a file folder in the desired location, opening the MO2 Settings interface (as above), selecting the Paths tab, and altering the Downloads path to match the newly created file folder.

Mod Organizer 2: Base Profile Creation

With Mod Organizer 2 installed and correctly configured, it is time to introduce the creation of Profiles, one of the signature features of Mod Organizer 2. Profiles are used to create mutiple 'versions' of your mod installs, which allows for anything from multiple versions of an install to shorter installs in support of merges (one of the primary things this guide will use it for). This step will familiarize you with the creation of profiles for later in the modding process.

Special Instructions:

  • Mod Organizer 2 is currently using a "Default" profile. A "Vanilla" profile needs to be created to establish a working game baseline and for troubleshooting purposes.
1. Locate and press the Configure Profiles button (most MO2 themes show this as an icon that looks like an ID card, but can vary).
2. In the Profiles Window, select Create.
3. In the pop-up, type Vanilla Skyrim SE.
4. Ensure that the Default Game INI Settings checkbox is unchecked.
5. Select OK.
6. Verify that Vanilla Skyrim SE appears in the list on the left.
7. Verify that the Use profile-specific Game INI Files is checked.
8. Click on and highlight the Default profile.
9. Click on Remove.
10. In the pop-up that appears, select Yes.
11. Exit the Profiles Window by pressing Close.
12. Verify that Vanilla Skyrim SE appears as the selected profile (shown above the mod list aka "the left pane").

Setting up Base Tools for Mod Organizer 2

The last major step is to setup some of the previously installed tools to work from within Mod Organizer. Running these tools via Mod Organizer 2's launcher will allow the other tools to make use of the Virtual File System and see the files from the installed mods as the game, itself, will when it is loaded.

Some programs that have been installed will be automatically detected by MO2, including SKSE, Skyrim, the Skyrim Launcher, LOOT, and the Creation Kit. These will appear in the MO2 Launcher (just above the right-pane) and are pre-configured.

Special Instructions:

  • xEdit, Mator Smash, Wrye Bash, and zEdit need to be setup with Mod Organizer 2.
1. Locate and press the Executables button (most MO2 themes show this as an icon that looks like a gear, but can vary).
2. In the Title line, enter SSEEdit.
3. In the Binary line, click the [...] button at the end of the line.
4. In the Windows folder that opens, navigate to and double-click on SSEEdit.EXE in its installed location.
5. Ensure no optional checkboxes are checked.
6. Click the Add button. SSEEdit should appear in the list at the top of the window.
7. Repeat steps 2 through 5, entering "SSEEdit - Quick Auto Clean" as the Title. This second instance will be used only for cleaning of plugin files, and will be explained further later in the guide.
8. In the Arguments line, add -quickautoclean.
9. Repeat step 6. SSEEdit - Quick Auto Clean should appear in the list.
10. Repeat steps 2 through 6 for Mator Smash, Wrye Bash, and zEdit, selecting the appropriate binary in each case. No arguments are needed for these entries.
11. After all programs have been added, click on Close on the Modify Executables window.