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:

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.

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.