Step 3 – Mod Organizer 2 and SKSE64


Now it's time to set up the best mod managing tool ever! Of course I'm talking about Mod Organizer 2, the updated 64bit successor to Classic Skyrim's Mod Organizer with tons of advanced features and the invaluable virtual data folder system. We will also configure all the options, link your executables to MO2 and install the Skyrim Script Extender for Special Edition (SKSE64).

3.1 Installing Mod Organizer 2

  • Download the latest version of Mod Organizer 2 (Archive version).
  • Extract the archive to a new folder on the same hard drive as your Skyrim SE installation but outside your C:\Program Files x86 and C:\Program Files folders.
  • (Optional) You can add shortcuts of ModOrganizer.exe to your taskbar and modding folder if you wish since from now on you will always launch Skyrim SE via MO2.

  • Run ModOrganizer.exe.
  • A window will come up - select 'Portable'. This is very important and means all sub directories will be located inside the root folder which is required for some modding tools to work (and also for simplicity and convenience).
  • Next you will be asked which game you would like to mod. Normally, MO2 should recognize your Skyrim Special Edition installation so select that in the list.
  • If you never worked with MO2 before, it would now be a good idea to accept the tutorial prompt that should come up next. You will be guided through the basic features of MO2.
  • Confirm when asked to associate NXM links with MO2.

3.2 Configuring Mod Organizer 2

We can see that the five ESM files in the load order (right panel) are already in the correct order and sorted by priority - so far so good!

If you click on the executables drop-down list in the top right, you will see that both SkyrimSE.exe and SkyrimSELauncher.exe as well as the CreationKit.exe are already associated with Mod Organizer 2. That's great! In order for MO2's virtual data folder to work, you must launch all modding tools and the game itself through MO2 by selecting the application in the drop-down menu and hitting Run.

  • When you're ready to move on, open the Settings by clicking the crossed-tools-icon in the top left icon bar.
  • In the Nexus tab, you should enter your log-in credentials and check Automatically Log-in to Nexus. Upon downloading your first mod from the Nexus via the 'With Mod Manager' option you will be logged in (in Mod Organizer 2).

You can now configure the UI to your liking. I always drag the log at the bottom all the way down to hide it, then re-arrange the proportions of the two panels. By right-clicking the top of the left pane, you can choose what to display in your mod order: For me, that's Flags, Content, Category, Source Game, Version and Priority. Category and Version aren't important but you definitely need the others displayed.


3.3 Managing mod downloads with Mod Organizer 2

Most people are probably using the 'With Mod Manager' download options on the Nexus, having their preferred mod manager load up the file with all the data (like version number and Nexus ID) and then install it through the mod manager's UI. That is the fastest and simplest way so we'll set up Mod Organizer 2 for that.

  • First we need to associate the 'With Mod Manager' links with Mod Organizer 2 if you haven't already confirmed this during the installation process.
  • To do so, open the Options window, switch to the to the Nexus tab and click Associate with "Download with manager" link.

  • Then switch to the Paths tab where you need to change the Downloads directory.
  • Since we installed MO2 as a portable application, all your mod archives would normally be downloaded into a sub-directory of the root folder - which in turn may (should) be located on your SSD or otherwise fastest hard drive. These are only the mod archives which are then extracted so after the installation, they only use up space. However, keeping the archives as backups is a good idea since mods are regularly taken down from the Nexus or a different, older version gets removed.
  • This is why we created the ARCHIVE in our modding folder! Point the Downloads location now to your ARCHIVE folder which is already somewhere with lots of free space. The downloaded mod archives will be saved there from now on.
  • Occasionally you will have to download mods manually (SKSE64, everything related to ENBs, ...). You can just move them into your ARCHIVE folder as well if you like, then everything is in one place.

3.4 The Mod Organizer 2 Core Profile

For each section in the installation of The Phoenix Flavour we will create a seperate profile. That way you can easily go back to a working Core / Core + Visuals setup and copy them to base a new setup off of them.

  • Create a new profile now by clicking the ID-card-icon in MO2's top left icon bar.
  • Hit Create and enter The Phoenix Flavour - Core as the profile's new name and make sure Default Game Settings is not ticked as that would prevent MO2 from importing your edited INIs. Then click OK.
  • Next select your new profile in the list and check Local Savegames. The second option, Local Game Settings, should be ticked by default which is important - this causes your imported INIs to be profile-specific. Later on, you can use MO2's INI editor to tweak your INIs for your Visuals profile without affecting the 'clean' Core INIs.
  • Finally close the Profiles window and select your new profile in the drop-down menu.

3.5 Installing the Skyrim Script Extender

SKSE64 is a hard requirement for a large amount of mods, most importantly SkyUI and its mod configuration menu (MCM). It is absolutely essential for every mod setup.

  • Download the build for the currently supported version of Skyrim SE here or - if the guide is not running the latest binaries - here.
    • skse64 2 00 12.7z
  • Extract the archive's contents to Your Modding Folder\temp. Move the following three files into your Skyrim root folder:
    • skse64_skyrim version number.dll
    • skse64_loader.exe
    • skse64_steam_loader.dll
  • You can delete the remaining loose files (readme and whatsnew) and also the src (source code) folder.

  • Right-click the Data folder and select Add to archive. Rename the archive to something like: SKSE64 - Data v2.0.x [Main File].
  • Switch to Mod Organizer and click the hard-drive-icon in the upper left icon bar to install the new mod. Navigate to your temp folder and double-click the new archive.
  • It will then be installed as a mod in MO2. Make sure it is ticked in the left pane. You can now delete the folder and archive in your temp folder.

  • Finally we need to add the executable - skse64_loader.exe - to Mod Organizer 2.
  • Click on the gears-icon in the upper left icon bar to open the executable configuration.
  • In case MO2 has not pointed SKSE at the skse64_loader.exe in your root folder yet, do this now by clicking on the button next to Binaries.

3.6 The SKSE.ini File

  • Download my SKSE.ini from the file section and install it as a mod through Mod Organizer 2.

3.7 Verifying that SKSE64 is installed correctly

To test whether SKSE64 is now working as intended, select the SKSE64 Launcher in the drop-down menu and hit Run. Once you are in the main menu, open the console by pressing the tilde key (~) or ^ (should be right next to 1 on your keyboard) and type:


Once you hit Enter, it should return the latest version number. To quickly close the game, just type qqq in the console and hit Enter.