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{{Notice| These directions are part of a much larger document, "Lexy's Legacy of the Dragonborn: Special Edition", a modification guide directed at players of Skyrim: Special Edition by ''Bethesda Software''. As such, there will be references to other programs and practices that are not covered in this snippet. I have been working on this guide, doing a complete re-write of the guide for clarity and accuracy, as Lexy (the original author of the guide) has a bad case of dyslexia, so her ability to write in plain English is somewhat impaired. For the purposes of the assignment, please keep in mind that there are many steps here that you may not want to perform on your own computer system (and in fact may not be able to perform without Skyrim installed to your system).}}
[[File:LOTDSE Logo.png|frameless|center|800px]]
[[File:LOTDSE Logo.png|frameless|center|800px]]
= <span style="color:#00ff00">Installation and Setup of Mod Organizer 2</span> =
= <span style="color:#00ff00">Installation and Setup of Mod Organizer 2</span> =

Revision as of 23:09, 29 June 2019

LOTDSE Logo.png

Installation and Setup of Mod Organizer 2

This guide was written specifically for use with Mod Organizer 2 and it's in-built functionality. Some guide users have reported success using alternate mod management systems, but any attempts to use alternative mod management systems are unsupported by Lexy or the Guide Development Team.

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. There is no workaround 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 often.
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 website (one of the largest mod repositories on the internet, and the primary source of mods used in this guide) and for user comfort. Throughout these instructions, example icons for MO2 will be shown using the Paper Dark Theme - most themes use identical icons, but due to the number of possible themes, not all are shown. The theme will also be set by the user in this step, so more information on this later.

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 or by pressing the Nexus Icon in the toolbar. 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 accounts, with no bandwidth cap, are available. Details can be found on the NEXUS website.
EX: Darknexus.jpg
2. In the toolbar of Mod Organizer 2, locate the 'Settings' button. 
EX: Darksettings.jpg
3. At the top of the window that appears, press on the Nexus tab.
4. Click on the Connect to Nexus button.
5. If you are not logged into the Nexus, you will be prompted to do so at this time.
6. 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.
7. 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. 
EX: Darksettings.jpg
2. At the top of the window that appears, press on the General tab (if not already selected).
3. In the upper right corner of the Settings window, locate the Theme drop-down (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. 
EX: Darkprofiles.jpg
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.
EX: Darkexecutable.jpg
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.

Mod Organizer 2 is now fully installed and configured, ready to be used to install the modification list.


  • All icons shown are from Mod Organizer 2, a freeware creation by Tanin and the MO2 Team, available on the NEXUS.
  • The Lexy's LOTD Logo was created by Brian "Shadriss" Goodrich for use with Lexy's Legacy of the Dragonborn: Special Edition mod guide.
  • All other names, abbreviations, and programs mentioned are the property of their respective owners.