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 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.

Special Instructions:

xEdit, 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. A Pop-up box should appear press the + (Add an executable) button.
3. In the Pop-up box select "Add from file.."
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. Select "apply" at the bottom right of the pop-up.
7. Repeat steps 2 through 6, selecting "SSEEdit – Quick Auto Clean.exe" file from the installed location. This second instance will be used only for cleaning of plugin files, and will be explained further later in the guide.
8. In the Argument field of  "SSEEdit – Quick Auto Clean" add -Dontcache
9. Repeat steps 2 through 5 for Wrye Bash and zEdit, selecting the appropriate executable file in each case. No arguments are needed for these entries.
10. After all programs have been added, click on "Okay" on the bottom right of the Modify Executable window.

Mod Organizer 2 will have automatically detected the three official DLC files for Skyrim, but will have them ordered alphabetically, which is not desired. Note also that they will be listed as "Non-MO" under the Category heading - this is an indication that the files are located in the Skyrim base directory. These should be the only files with this listing through the entire guide... if you see it again, you have incorrectly installed a mod.

Special Instructions:

Initial detection of Skryim DLC will place them in an incorrect order.

1. In the left pane, drag-and-drop the three DLC files into the following order (top-to-bottom): Dawnguard, HearthFires, Dragonborn.

The loading order of Skyrim DLC is incorrect and needs to be correctly sorted.

1.  From the drop-down Executables list (right-side, above the plugins list), select LOOT.
2. Press the Run button.
3. Once LOOT has finished loading, locate the "Sort" button in the top right corner and click on it. Its icon is three horizontal lines above each other.
4. LOOT will automatically download any updates to its masterlist. It will then compare the files it sees (which is only the DLC at this point) to this masterlist files and sort them into a proper order. Additional messages will be displayed after sorting that indicate that there are ITMs and Deleted References in these files. See the notice below for an explanation of these two terms.
5. Click Apply to accept LOOT's generated load order. If no changes were made (which happens on occasion), the Apply button may not appear. This is normal, and of no concern.
6. Close LOOT by using the X button in the top right corner of the LOOT window.

This process has taught you two processes:

• Loading of LOOT via Mod Organizer. This same process applies to all programs loaded via MO2, and will not be repeated in other steps during the modding installation process. If a tool needs to be loaded in any other fashion, those instructions will be noted when needed.
  *Sorting of a load order using LOOT. This will only be done once more (officially) in the guide, near the end of the process. However, this process is universal to ANY mod list, and can be applied in many other circumstances.

The Vanilla Skyrim SE Profile is now properly set up. This profile should be kept for possible troubleshooting purposes, but otherwise left alone.

1. Using the directions provided previously to create the Vanilla Profile, create a new profile with the name "Legacy of the Dragonborn - Special Edition" (or another name of your choosing).

1. Ensure that the newly created "Legacy" profile is selected at the top of the left pane in Mod Organizer 2.
2. In the MO2 toolbar, locate and click on the "Install a new mod from an archive" button (will look like a file folder in most themes).
3. In the window that opens, navigate to the location of the SKSE file downloaded earlier. Click on it to highlight it.
4. Click on Open.
5. In the next window that appears, replace the text (if any appears - sometimes there isn't any) with SKSE Scripts. This is the name that will appear in the left pane of Mod Organizer 2 after installation.
6. Another window will appear, as the SKSE archive is not properly set up for an automatic installation. If this is the first time you've seen this window (and we assume it is), MO2 will give you a quick tutorial on how to use this tool. Read it to help with understanding the following instructions.
7. In the file tree, navigate to and highlight the Data folder inside the archive.
8. Right-click on Data.
9. In the right-click menu, select Set Data Directory. The display should change to show only a Scripts folder, which should be checked. A green "Looks good!" will appear at the bottom of the window if you have done this correctly.
10. Select OK.

A new entry should appear in the left-pane with the name given it above and an empty checkbox next to it. This indicates that it has been installed but not activated. Also note that MO2 does not have a version number or category set for this mod - neither are required, but if you wish to fill these in, you can do so.

1. Right-click SKSE Scripts (or as appropriate).
2. In the right-click menu, select Information.... Alternately, you can also double-click the mod name to achieve this as well.
3. In the Categories tab, locate and place a checkmark next to Utilities.
4. In the NEXUS Info tab, set the version number to the installed version of SKSE (as annotated in the SKSE download earlier).
5. In the NEXUS Info tab, set the Mod ID -1. This tells MO2 that the installed files were not provided by the NEXUS, and will prevent MO2 for searching the NEXUS for data and update information (among other things).
6. Click Close to save and exit the window.

SKSE is needed to run many mods this guide uses. Proper installation needs to be verified.

1. 1. Run Skyrim:SE by using the SKSE Executable in MO2.
   2. After the game has loaded into the main menu (listen for the Skyrim Theme to play), open the console with the ~ key (by default). This is the key directly above the TAB key on most keyboards.
   3. In the console that opens, type getskseversion and press enter.
   4. Verify that a new line appears in the console, indicating the version of SKSE you have installed. If there is no output, or a version other than the one you installed appears, reinstall SKSE with the correct files or verify correct installation against the instructions provided above.
   5. Exit Skyrim.

We begin the modification process by altering some of the vanilla game files. Bethesda, like a number of modders, have created unintended duplication of records in their DLC files. These records are referred to as Identical to Master records, or ITMs. In most cases, these are not inherently game-breaking, and usually can be ignored if one is playing a mostly vanilla game. For a heavily modified game, however, they can have undesirable effects.

Another issue, and one that is far more serious, are deleted records. These can cause Crash to Desktop (CTD) errors, and should always be cleaned from plugin files.

Both ITMs and UDRs exist in the Bethesda DLC content files, and will need to be cleaned. Note that the below process is universal to this process, and will not be repeated for other mods that require cleaning.

Cleaning Instructions:

Create a backup of the original files.

1. Navigate to ...\Skyrim Special Edition\Data.
2. Copy-Paste the following files to your desktop or other readily available location: Update.esm, Dawnguard.esm, HearthFires.esm, and Dragonborn.esm.

The games files contain ITM and UDR records, and require cleaning.

1. Start Mod Organizer 2, if not already running.
2. From the drop-down executables menu, select SSEEdit - Quick Auto Clean. Ensure this is the xEdit version with Quick Auto Clean, as this is the one that will handle the removal of ITMs and UDRs.
3. Press Run.
4. In the file selection menu that appears, check the box next to Update.esm and no other files. If any additional files need loading, xEdit will automatically load them.
5. Click OK.
6. xEdit will now run the cleaning process automatically.
7. Wait for the process to complete, indicated by the appearance of the message Quick Clean Mode finished.
8. When the message has appeared, close xEdit by clicking on the X in the title bar of the application ("X-ing out").
9. Repeat steps 2 through 8 for Dawnguard.esm, Hearthfires.esm and Dragonborn.esm.

1. From the drop-down executables menu, select SSEEdit. Ensure this is the xEdit version without Quick Auto Clean.
2. Press Run.
3. In the plugin selection window, right click.
4. In the right-click menu, select Select None.
5. Place a check mark in the box next to Dawnguard.esm.
6. Select OK. Dawnguard will now be loaded into xEdit, along with any other required files.
7. After all plugins are fully loaded, click on the "+" next to Dawnguard.esm. Its file tree will expand.
8. Locate and press the "+" next to Cell. Its sub-records will appear.
9. Locate and press the "+" next to Block 5. Its sub-records will appear.
10. Locate and pres the "+" next to Sub-Block 3. Its sub-records will appear.
11.  Locate and click on 00016BCF. The right pane will now display all records associated with this cell record.
12. In the right pane, scroll down and locate the XEZN sub-record that refers to RiftenRatwayZone [ECZN:0009FBB9.]
13. Right click on the above record in the "Dawnguard.esm" column and select Remove. A window may appear warning you that you are making a change to the file – when able, allow the change.
14. Do the same for Block 2 -> Sub-Block 1 -> 0001FA4C  CWGuardTempates (the entire record).
15. Block 8 -> Sub-Block 1 (the entire sub-block).
16. Close xEdit and save by clicking the "X" in the program's title bar.

While BethINI does handle the vast majority of the tweaks needed to the INI files, a few need to be changed manually. This will be done via MO2's INI Editor. To access the viewer, click on the Tools icon in MO2's toolbar, then select the INI Editor. Once open, make the following changes (if the option does not appear, add it):

[Grass]
bGrassPointLighting=1

[SaveGame]
bDisableAutoSave=1
bAllowScriptedForceSave=0
bAllowScriptedAutosave=0

[Display]
bSAOEnable=1

[Main]
bSaveOnPause=0
bSaveOnRest=0
bSaveOnTravel=0
bSaveOnWait=0

Due to the heavily modded nature of this guide, it is advised to have autosaves turned off and to create fresh new saves every time and not overwrite old pre-existing saves.

SkyrimCustom.ini is created by BethINI and can be used to overwrite settings placed in Skyrim.ini. For the purposes of this guide, we will use a blank copy of this file placed in the Legacy Of The Dragonborn - Special Edition profile that you will use to actually play the game.

Before you can edit the SKSE.ini file, you will have to create it.

1. Right-click SKSE Scripts in the Mod Organizer mod list.
2. Select Open In Explorer.
3. Create and enter a folder named SKSE.
4. Create and open a text file named SKSE.ini. Make sure you are showing hidden file extensions.

Once this file is open to be edited, paste in the following:

[General]
ClearInvalidRegistrations=1

[Display]
iTintTextureResolution=2048

This enables self-healing of rogue updating scripts in saves.

Save and close SKSE.ini then exit explorer.

In this section you will set up zMerge so that you can create merged mods later on.

1. Open zEdit and select zMerge from the drop-down menu.
2. Press Start Session.
3. Click on the cog in the upper-right corner and a new popup box should appear.
4. Navigate to Integration Settings.
5. Under Mod Manager select Mod Organizer 2.
6. Under MO2 Instance select Portable.
7. Under Mod manager path, fill in the file path to your main Mod Organizer 2 folder.
8. Under Mod manager mods path, fill in the file path to your Mod Organizer 2 mods folder.
9. Navigate to Merge Settings.
10. Under Merge output path fill in the file path to where your Mod Organizer 2 mods folder is.
11. Uncheck Disable plugins.
12. Navigate to Archive Creation Settings.
13. Under Advanced change Minimum files per archive to 999999.
14. Under Advanced make sure Create texture archives is unchecked.
15. Click OK.
16. You can now close zMerge.

Check these pictures on how to set up zMerge if you're having trouble.

A Special Step is required for users that connect their GPU and Monitor Via a HDMI Cable.

For Nvidia users:
Go to your Nvidia Control Panel (right click on your desktop)
Then go to "change resolution" and find "Output Dynamic Range" and change it to "Full". (if it is grayed out press "Use NVIDIA color settings" first)

For AMD users:
If you're using a AMD/Radeon graphics card you need to do a similar tweak, but you have to change the display pixel format instead. This can
be done by selecting "RGB 4:4:4 Pixel Format PC Standard (Full RGB)" instead of the default "RGB 4:4:4 Pixel Format Studio (Limited RGB)" inside of the AMD Catalyst.