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STOP Your Mods From CRASHING | Mod Organizer 2 Skyrim SE Guide (Part 2)

Ok, the mod list, this is the left pane of your MO2 window and I have referred to it by many names throughout the course of my guides but the final name I will be settling on is mod list. What you need to know is that not only is it a list of all the mods you’ve installed through Mod Organizer or any other means but it is also a dynamic installation order. What do I mean by this? Basically if you were installing mods to your Skyrim data folder manually or through the use of older mod managers like Nexus Mod Manager, you would be overwriting asset files from conflicting mods in your data directory with mods installed last overwriting those installed first. 


The modlist is no different in that regard, the assets of mods towards the bottom of the list will overwrite any that are above them. The only difference is, because of the virtual file system used by MO2 (which essentially compiles your data folder at launch) redundant files are always kept in their separate mod data folders. This is unlike other mod managers that delete overwritten files from the data directory and revert them back if mods are uninstalled. Also keep in mind that just like we talked about in the LOOT video, the modlist does not effect plugin load order or which plugin records overwrite each other. Just surface level file name conflicts between assets like scripts, meshes, textures etc. 

Modlist Navigation

So let’s talk about some of the very powerful features that the modlist has. Obviously the first thing you can do is enable or disable mods from loading into your game by checking the white square located on the left side. You can also drag and drop mods around to change your installation order any time you wish. Again, this allows assets like textures, meshes and scripts to overwrite each other with the assets contained in the lowest mod being dominant. To quickly see if a mod has any conflicting files simply look at it’s flags. 


If you see a yellow lightning bolt with a plus beside it that means that the current mod has files that are overwriting another mod. A yellow lightning bolt with a minus sign means that it has files that are being overwritten by a different mod. Obviously both plus and minus mean that it contains both overwriting files and contains files that are also being overwritten. You can see which specific mods are doing the overwriting and are being overwritten simply by clicking on the mod in question. MO2 will highlight mods with overwritten files in green and mods with overwriting files in red. These can also quickly be seen in the mod list pane scrollbar. 

Conflicts Menu

If you double click on the mod in question and go to conflicts, in the general tab you can see a much more detailed list of asset conflicts. The upper list shows any files that are being overwritten by the mod you are looking at and the middle list shows any files from this mod that are being overwritten. If you hit the bottom most drop down arrow you can also see any assets that don’t conflict with other mods.

Counters for these files are also provided so you can quickly see how many there are in each category. If you click on the advanced tab you can see a complete list of files included in the mod in one list and their conflicts or lack thereof. You can also search for specific files or apply filters to the list. Additionally, you can also hide any file from the conflicts tab by right clicking it and selecting hide, this will prevent it from being loaded in game and cause the preceding mod’s file to show up instead if there are no other overwrites.

Additional Flags

Back to modlist flags though, a few other noteworthy ones include a white lightning bolt which means that all files in a given mod are being overwritten effectively rendering it useless in your mod order. A green chess piece with a question mark which denotes that a certain mod has come from a Nexus page different from game you are modding. That one in particular comes up often when modding Skyrim SE as some Original Edition mods are compatible with Special Edition or can become compatible through minor tweaks so you may want to use them in your game. If you don’t port them properly however, they can cause crashes so be careful when doing that.

The other one you’ll see a lot is a heart with a question mark which means you haven’t endorsed a mod you are using. To remove it simply right click the mod and hit endorse. If there are any flags you don’t recognize you can simply hover over them and a description will pop up telling you why they are present.

Version Checking

The other big feature of the mod list is that it includes the version number of each mod you have installed from Nexus. The unfortunate limitations of this are that mods that aren’t downloaded from Nexus or installed manually won’t include their version number but instead their installation date. This can however be changed by double clicking on the mod, going to Nexus info and entering the information manually in version. While we’re here, you can also edit the mods Nexus ID if ever it’s incorrect and you can also read it’s description, though I just suggest hitting the open in browser button instead. 

The other problem with version numbers in MO2 is that some mod authors can have different versions of their mod for different mod setups, ENBs are a good example of this, and this can cause MO2 to flag the version as red despite it being correct for your load order. You also need to tell MO2 to check the versions for installed mod manually by clicking on the screwdriver and wrench dropdown menu and selecting “check for updates”. 

Warning About Updating Mods

Just a warning about updating mods guys: even if you do have an outdated version of a mod, that doesn’t mean you need to update it. If your setup is working fine it may just be better to leave your setup as is. If the latest version patches a bug or something it’s definitely a good idea to update but if its a large release that changes lots of things about a mod, it may create new conflicts for your load order. For that reason it’s always a good idea to read over the latest patch notes in the readme files or Nexus description and considering how the changes could affect your load order before updating.

Category and Priority

The other two filter headers are category and priority, those should be self explanatory. Categories are just the Nexus categories each mod is grouped in. This again can be easily changed by double clicking the mod, going to the categories tab and checking any category you want to apply then selecting the primary category at the bottom. Priority is the mod’s position in the mod list, i.e it’s installation position. This is how the mod list is sorted by default. You can access more sort filters by right clicking on the filter header and checking or unchecking any you see fit.

Mod Menu

Let’s move back to the mod menu for a second and go over everything we’ve missed. That’s the menu you get when you double click any mod in your list. The first tab allows you to view any text files included in a mod, this is handy for quickly glancing over readmes. You can also edit and save them directly from MO2. If you ever set up your own personal conflict log for your playthroughs, this makes it really easy to write down any issues you find. Also if you see any “open in explorer” buttons from here on out, those allow you to open the location of the file in file explorer.

The INI files tab is the same text editor from before the only difference being that it only shows INI files. Images shows any pictures that may be included in a mod. These used to be fairly common to show comparison shots but are less frequent today because of the image galleries on Nexus. 

Optional ESPs

Optional Esps is a tab that you may find yourself using from time to time. By moving any available ESPs installed in a mod into the optional section, you can hide the plugin from MO2 which will prevent it from being loaded in game or showing up in your load order. Unfortunately any ESPS set to optional, are independent of any profiles that you have created, so hidden plugins remain hidden in all your profiles which could cause issues if you forget about any plugins you may have hidden this.

If you have a mod merged with a patch plugin, that is required for one profile and not another I would just suggest installing two versions of the mod, one with and one without the patch then enabling or disabling it in both modlists. This will remove any manual tweaking. Where you might find this useful though is when installing something through a FOMOD and you find a patch for a mod you plan on installing later. Rather than halting the install process to install the other mod you can install the patch and hide it, then install the other mod when you wish. You can then move the patch back into available ESPs when you’re ready to use it.


The notes tab allows you to write personal messages about any mod you have. You can write small comments at the top that show up in the notes column of the mod list, if it’s enabled but longer notes can also be written in the bottom text box and can be seen when hovering over a mod’s notes column or flag column.


The last tab, filetree, shows every file located in a mod the same way you would see them in file explorer. Open any files through your default run program by right clicking and selecting open/execute. You can also do most other things you can do in file explorer like create folders, rename files and delete files. Also included is a way to hide any file or folder from here as well. Lastly if you are unsatisfied with MO2’s file management interface, you can open any file or folder in file explorer using any of the open in explorer buttons.

Mod Menu Customization

The final thing I want to show you about the mod menu is that any tab can be dragged around and repositioned with the first tab opening by default. Because I use the filetree tab so much, I like to place it first to avoid unnecessary clicks but you can rearrange them in whatever way makes sense to you.


Perhaps one of the biggest features of MO2 is the fact that you can have multiple mod lists through the use of profiles. These can be accessed just above the mod list pane via a dropdown list. You can create profiles through the use of the toolbar profiles icon as mentioned in the last video or through the manage button in the dropdown list. When you select a different profile, the list of enabled mods will change and you can independently rearrange the lists from one another.

Profiles and versatile installation order management are incredibly powerful when used in tandem to resolve mod conflicts. Even if you don’t know what any of your mods change in-game, you can find the one or two mods that are the source of the conflict simply by duplicating your main profile and applying trial and error and the process of elimination. By slowly disabling active mods and testing the issue ingame, you can find the problematic mods on your test profile then make any appropriate changes on your main profile by installing a patch or removing one of the mods entirely. 

All to often, I find that people have an issue with their game and choose to reinstall everything, starting over from scratch, but this is something that is simply not necessary with MO2. While you may have to restart your save game if it is corrupt, you don’t have to redownload all your mods and waste 10s of hours only to get back to where you were. Back in the Nexus Mod Manager days, sure that may have been the quickest thing to do but remember that MO2 doesn’t even touch Skyrim’s data folder so reinstalling the game doesn’t change anything. You’re just scraping your mods and starting over for nothing.

It’s much easier to actually find the troublesome mod or mods then figure out how to resolve the conflict by say asking on my Discord. Here’s the cool thing though, even if you do want to start over, a vanilla game is just a few clicks away: simply create a new profile and untick everything in its mod list. Don’t waste time, uninstalling the game or MO2 in an effort to fix your problems, remember we did that once already at the start of these guides.

Above the Modlist

Ok, let’s go over the rest of the buttons above the modlist.The screwdriver and wrench dropdown allows you to easily edit the modlist by enabling or disabling all visible mods. These buttons couple nicely with the bottom filter which allows you to search for mods, just be sure not to touch these when you’re viewing your entire mod list. In the same dropdown you can also install a mod manually, create an empty mod and create a separator.

Empty mods are useful for storing generated files, from mods like Fores New Idles in Skyrim or PerMa and separators allow you to visually separate the mod list for yourself. Under the screwdriver and wrench dropdown you can also find a refresh button for the GUI, this is useful if you’ve installed a mod the the MO2 mods folder manually and need the mod list to update within MO2. Finally, you can also find a button to export your mod list to a Comma Separated Value file which is basically a written spreadsheet of your mod order.

The folder dropdown is an extremely useful as it contains navigational shortcuts to file explorer for every folder associated with modding your game and currently active profile. That means as you select different profiles certain shortcuts like those to your INI files will update, because MO2 has profile specific INI files. Basically everything except your personal mod utilities folder is here so definitely use these and save yourself some time.

Backup and Restore Mod Lists

The final two buttons allow you to backup and restore your mod list. These can be an alternative to duplicating your profile in the process of resolving mod conflicts or when testing newmods. I personally just use profiles when doing this as it makes the most sense to me but it’s there if you prefer it. It’s also a good middle ground if you just want to test one or two mods, I think. To use these hit the blue arrow button to backup your current profile and the yellow arrow when you’re ready to restore it then select which backup to restore.

Mod Counter

Just right of the backup buttons you can find the active mods counter for your selected profile. If you hover over this value, you can see specific details how many total mods there are, how many are dlc, how many are separators and how many mod back ups you have. We’ll go over creating those in just a minute. You’ll also notice that there are two categories, all and visible. The visible values change as you filter mods in the bottom search filter.

Right Click Menus

Alright, let’s go back to the mod list for a minute and check out the right click menu. When you right click a mod in the list an action menu will appear which offers many of the features we have covered already. Under “all mods” you can find the same buttons you have in the screwdriver and wrench dropdown, you can change the selected mod’s categories and primary category, and force check the mod for updates. You can also enable or disable all the selected mods that you’ve shift clicked or ctrl clicked on. Selected mods are highlighted in blue.

Using send to you can move selected mods to the top or bottom of your list or even a specific priority location or category. The right click menu also allows you to rename, remove or reinstall a mod and has quick links to it’s Nexus page and location on your drive. You can also create a backup of any mod here. Rightlicking a backup in your modlist will allow you to restore or remove it. If you’re going to be playing around with the files of any specific mods, backing them up first is always a great idea, as they are not profile specific. Finally, right clicking on a separator will allow you to rename or remove it and change its color.


Alright we’re getting close, now let’s finish up by talking about what’s below the modlist. The search filter obviously allows you to search for items in the mod list but what you may not have known is that you can search for multiple items through by using the pipe character to separate your search terms. The pipe is the vertical line located just under your back space if you didn’t know. So if I wanted typed in something like “SkyUI | SKSE” everything that contains SkyUi or SKSE will appear in the mod list. You can repeat the pipe multiple times in your search too.

The groups dropdown to the left of the search filter gives you alternate ways to sort your mod list. I’ve never used anything besides no groups but if you use it or know why it would be useful let me know down below.


Finally the leftmost filter area allows you to view filter categories for your mod list. Many of these are just Nexus categories however there are also MO2 specific categories based on either their state in the MO2 mod list or the files they contain. The MO2 specific category filters are denoted by their angle brackets. You can select one by simply clicking it or multiple by ctrl clicking. For instance let’s say I wanted to see checked mods that also contain INI files that are listed under environment on Nexus. I would select those 3 criteria and as you can see the only mod that fits all of those for me is Obsidian Weathers and Seasons. But now let’s say I wanted to see mods that just contain INI files or were environmental. I would control click <checked> to remove that from the filter and hit the or bubble at the bottom. Now I can see all my mods that contain any of the selected filter categories. To clear the filters I can simply hit clear or clear all filters below my mod list. Be sure to tick back the and bubble so you don’t end up with an empty mod list.

Why This is a BIG Deal

As you can see, with MO2 the methods for filtering and searching mods are nearly limitless and irreplaceable when it comes to troubleshooting or tinkering around with your mod list. Doing something like filtering all your SKSE dependent or scripted mods is something you can’t do with Vortex but is two clicks away in MO2. Yet another reason to use MO2 over any other Mod Manager out there.

Hopefully after watching this video you know how to navigate your way around the MO2 modlist a little better. It’s kind of a lot to take in I know but just remember this video for the future when you’re trying to find a specific feature in MO2. In the next video we’ll be talking about the right pane and all the tabs included in it. At that point, you’ll know just about everything in MO2 and we’ll be able to get into the more nitty gritty aspects of modding, from LOD generation to automated patchers and manual record editing.

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