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Fix 90% of Mod Conflicts EASILY | LOOT Mod Organizer 2 Skyrim SE Guide

I’m sure most of you have heard the term load order while modding your game, be it on a forum, mod page, or even my own Discord. But what does it do, and why is it important? More specifically, how does it compare to mod installation order?

What is Load Order?

Let’s start with the first question. Load order is exactly what it sounds like, it is the order ESP files and ESM files are loaded into the game. This process occurs when you first start the game. Recall that these files are what tell the game what changes are included in a mod. If you need a better refresher of what these files do, and what files mods consist of, check out the MO2 intro video in the top right. You should have the information down pat, at this point. 

Alright well, the next logical question is why does the load order of these files matter? To answer that, let me give you a hypothetical. Let’s say you have 2 mods that change an NPC, Nazim for example. Well, the mod loaded last would get the final say in the changes. Sometimes, this kind of changes can cause game-breaking conflicts so a well-organized order can potentially remove many of these. But isn’t this conflict resolved by mod installation order? No. And this is where things can get a bit confusing.

Load Order VS Installation Order

To better understand the difference between load order and installation order, let’s break down game changes created by mods into two categories. The first type of change is one that is handled entirely by the plugin file, be it an ESM or ESP. Apart from that, these changes don’t need any other files to take effect.

The second type of change is one that is created with the help of other files, be it textures, meshes, scripts and so forth. These changes have pointers in the plugins that tell the game where the external files can be found. When we are dealing with installation order, we are only resolving the latter of these two types of changes. I.e only direct file name conflicts. With load order, on the other hand, we are dealing with the changes made internally, inside any of the plugin files we mentioned before. So, if plugins 1 and 2 both change Nazim’s clothes, only the plugin loaded last will have a noticeable effect in the game.

Now if that was confusing, bear with me because there’s a little bit more. Load order also affects the order BSA archives are loaded into the game. That means that if there are two identical files in each archive, the file contained in the last loaded plugin’s BSA will show up in-game. Again seriously go back and watch my MO2 intro video and really have these files memorized. Basically what this means is that first BSA archives are loaded followed by any loose files you may have. I.e. loose files always take priority over anything contained in a BSA  archive.

Load Order is Very Important

So if you got lost, that’s ok just go back in the video and take another listen. I still have a difficult time getting this stuff straight sometimes. Just do your best to go through a memorize this information as it really is the basis of what Bethesda modding is. If you can get this down you’ll have a much easier time resolving mod conflicts, troubleshooting and really just getting through frustrating modding moments. Alright so let’s hop into Mod Organizer 2 so I can show you where you can find your load order.

Load Order in MO2

In MO2 you can easily see the current load order of your ESMs and ESPs in the plugins tab of the right pane. If you click and hold any of the non-greyed out plugins you can actually adjust this load order by hand. The greyed out ones are part of the base game, so Skyrim, the DLCs and update are all contained inside your game folder. In the really olden days of Bethesda modding, before we had fancy load order sorting tools we would actually have to change this manually in the game’s launcher. That meant, actually knowing the changes created by each and every mod then organizing them so that no game-breaking conflicts occurred. Something completely doable with a few mods but a much more difficult task with hundreds of mods.

Now while you still really should know the overall changes made by each mod, this type of complete knowledge is not necessary anymore. Enter the Load Order Optimization Tool or LOOT for short. This handy little program brings down the mod information learning curve by automatically sorting your load order and arranging to best-fit something known as a load order master list.

How LOOT Works

The masterlist is exactly what it sounds like, at least kind of. If you were to take every mod that ever existed for Skyrim and you placed them all into one giant load order so that everything was in a “correct” location, you would have a LOOT masterlist. Now, this is in an ideal world. If you weren’t aware, Skyrim has a 255 plugin limit. Once you reach that point, the game simply won’t load so obviously there’s no way in hell you’ll ever end up using that many mods even with workarounds. Not that you’d want to.

Secondly, many mods simply just are not compatible with one another or cause major issues so you’ll just want to avoid using them together anyway. But if you’re a normal, smart user that makes sure their load order is free of such conflicts, you’ll find that using LOOT to sort your load order is actually really handy, especially when you’re a beginner or just someone that tests mods frequently. So this sounds great! Now let me fill you in on the real-world limitations of this tool.

Limitations of LOOT

Firstly, as far as I’m aware, each plugin in the LOOT masterlist is categorized on a case by case basis. If you know better, let me know, either way, it shouldn’t affect the validity of this point. What this means is that every time a plugin gets updated in any major and sometimes minor way, there is no way of being 100% certain with the use of LOOT alone that the masterlist information on that plugin is accurate, since something has been changed. Now sure, most updates won’t add anything big at this point in Skyrim’s modding years and some mods have reached final release but it’s still something to keep in mind.

The place LOOT gets a little more spotty I find is when it comes to patch plugins that resolve issues between one or two other mods. And if you’re using any sort of patch that you created yourself, like a Creation Kit mod, bashed patch or any other generated plugin–for me that’s PerMa, you can pretty much forget about LOOT sorting those without your help. You may not know what these are and that’s OK, I’ll be going into them in the future just keep this info in mind. The other thing is that you’re also sacrificing the neatness of a self-managed load order as visually, LOOT appears to be about as organized as a typical college undergrad.

LOOT is Awesome, Use It

Now with that out the way, I in no means want to discourage you from using this tool. In fact, if you’re a beginner I highly encourage you to use it as it dramatically lowers the knowledge curve when it comes to knowing what every single mod does that came it in the last 8 years. And in most cases, it will even save your butt by catching all the incompatibilities you missed because you didn’t read the posts tab on Nexus. Wink Wink.


Alright, that was extensive and long-winded. Let’s go ahead and install the damn thing. Head over to the official LOOT github at Hit the big download button and on the next page select loot.installer.exe. This is, of course, a tool, so it won’t be downloaded in MO2 even if you did get it through Nexus. Run the installer from your browser or downloads folder. Select your native tongue. Point the installer to where you want LOOT installed to. For us, that’s in our mod tools or utility folder, whatever you named it in the first video. Hit ok, and next. We’re not going to create a desktop shortcut since LOOT needs to run from MO2 anyway. And install. Go ahead an uncheck run loot because again, this won’t do anything for us. Go ahead and Finish.

Download: LOOT

Running LOOT

Now if we open up MO2, and check the executables drop-down box we’ll see that the MO2 devs were kind enough to locate LOOT for us. If for some reason LOOT isn’t there, add it like you would any other tool. Hit edit. Name it LOOT. In binary, navigate to the loot installation folder and select LOOT.exe and then add. Easy.

Before I go ahead and run loot let me just point out the sort button right here. I know it’s really accessible and clickbaity kinda like this video’s title but for the love of god please don’t use it. You’re getting none of the benefits from actually running LOOT in its entirety and it further obscures Load Order sorting which is by its nature is not a foolproof process. At least the full LOOT application actually points out serious mod conflicts and gives you some degree of control when sorting. Just go ahead and run LOOT from the executables list.

Alright, so now’s probably a good time to tell you that I have switched over to my actual load order for these tutorials. At this point, I figure you’re well informed enough to realize that everyone’s load order is different so as not freak when you see that my list of mods is entirely different from yours. If you’ve not done that yet, please do. Plus, I’m sick of switching game installs. Anyway, let’s go over everything a beginner like yourself needs to know about LOOT. Not that there’s much to it because LOOT has a pretty great interface.


Let’s go ahead and start by sorting, this is done with the 3 horizontal bars icon at the top right. When you do this, two things will happen. LOOT will automatically update it’s masterlist of mods and obviously sort your load order. Now, this is when most beginners click out and get to play their game. Don’t do that. Instead, look at the general information. This is essentially a brief overview of everything LOOT detected with your load order.

Obviously, masterlist revision and date is the version of your masterlist and it’s publication date. Total plugins are all the plugins in the virtual directory and active plugins are only the ones that will be loaded by the game. Total messages are all the message flagged by LOOT after it’s looked at your load order. That leaves the other 3, warnings, errors and dirty plugins messages as your main concern. If we scroll down we can actually see our plugin load order, it’s synced up with MO2 so what you see there is the same thing after you close the app.


Most messages you should see won’t have any highlights on them, these are just important information that you should read and consider. Not necessarily something that’s a problem. 


Warnings are highlighted in yellow and indicate issues detect by LOOT. They are usually easily fixable. Most of the time, warnings just tell you that you’re missing patches needed for 2 mods to work correctly. LOOT will actually tell you where these can be found and sometimes will even link you to their pages. The other type of warning is a dirty plugin notification. These should be cleaned with SSEEdit, I’ll talk about that one or two videos after this one so doesn’t worry if you don’t know anything about that yet.


Errors are really easy to spot, those are highlighted in red. These issues usually tell you that there are two mods that just don’t work together, and in that case, your best bet would probably do more research into them and figure out why they don’t work. Then, either uninstall one or live with the consequences. As you can see here, LOOT tells me the Immersive Citizens mod is incompatible with JK’s Skyrim. It even links us to the mod’s compatibility page. But that is is a load of bull. So take this an example of a time when LOOT is wrong. Remember at the end of the day, it’s your responsibility to catch these mistakes which is why I always suggest reading mod descriptions and posts.

Example of LOOT’s Limitations

Let me tell about what is going on in my particular case. While it’s true, that Immersive Citizens was not built to be used with JK’s Skyrim and that Immersive Citizens will not retain all of its functionality, the average individual would be very hard-pressed to find something out of the ordinary when using them together. This is one of those times where the LOOT developers are taking the mod author’s words as fact but what they don’t take into consideration is context.

You see, the mod author of Immersive Citizens actually claims all mods that alter the behavior of IC in ANY way are incompatible. While in one case he’s kinda right, I also think that he should tell users to decide on their own whether they are willing to accept the trade-offs. But then again, I also don’t have a mod with almost 4 million unique downloads so I don’t know what it’s like to be bombarded with questions from people that don’t do their own research… or do I..? Regardless, moral of the story is–LOOT isn’t an all-knowing machine. So read everything it’s telling you and decide for yourself if it’s accurate.

As you can see I have a lot of others warnings as well, most of them are for patches that I have merged so LOOT doesn’t detect those. The rest is dirty plugins that I’m keeping around for the SSEEdit video. So, now that I’ve looked over everything and made sure nothing is unaccounted for, I can click apply at the top and this will save the load order. 

Setting Manual Load Order Priorities

The final thing I want to show you is how to manually tell LOOT where to load plugins. This is handy for when it makes a mistake and loads a plugin before something it’s not supposed to. Of course, you can always do this in MO2 directly by clicking and dragging the plugins but then you need to do that again the next time you sort with LOOT. The easier thing to do is to click the 3 dot icon for the incorrectly placed plugin, I’m going to show this on the Dragonborn DLC even though it’s been placed properly, and select edit metadata.

As you can see a new menu shows up and if we select load after we can see a list of plugins that Dragonborn needs to be loaded after. LOOT already has Dawnguard and Hearthfires on the list but going to also add Update.esm by clicking the plus icon. After that, I type in update.esm in the filename and hit the floppy disk to save. Vwalla, now Dragonborn will certainly load after Update, again this wasn’t necessary as LOOT placed it correctly to begin with but now you know what to do when if it doesn’t. Dragonborn now also has a profile icon, showing that we’ve added our own custom changes.


At this point, we can close out of LOOT and we’re good to go. Obviously, there is more to LOOT so you can explore it further if you want but this is the most important stuff. I will have a video in the future going into everything LOOT has to offer but for now, this is it. Honestly, most won’t need to know much more than this anyway.

Go down below this video, give it a like, leave a comment and sub if you haven’t already. It helps spread these videos around the internet. Remember to check out my Discord to ask questions or just chat, there are some really cool people over there. Next video is to the left if it’s out and the overview of these guides is to the right. See you in the next one.


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