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What is next?

I've had the same problem during my last few play-throughs. I use item sorters, have been for years now. But it wasn't a problem until this last year or so.

In order to fix it, I simply used a console command to skip to the next stage, so I didn't miss anything and it didn't mess up anything either.

If I recall correctly, the command I used was:
setstage SS2C3_MA01 1000

That command will not "force complete" the quest, it just advances it to the next objective as if you had picked up the Stheno. I have also seen a few people mention that for them, the Stheno didn't actually spawn in. This happened to me once before as well. Making sure to save before entering that location could help avoid the missing weapon issue, at least for me reloading my save and entering the area again allowed the weapon to spawn as intended.
 
You also could try re-running your sorter if it's complex sorter. I wrote a post about this given the number of issues we've seen with folks who use item sorters. Basically if your item sorters are touching certain forms and items, then updates to the mod that are intended to fix bugs are basically being blocked by the sorters as they are overriding the item to reflect a previous version - https://www.simsettlements.com/site...ters-what-to-know-what-to-look-out-for.29981/
 
I've had the same problem during my last few play-throughs. I use item sorters, have been for years now. But it wasn't a problem until this last year or so.

In order to fix it, I simply used a console command to skip to the next stage, so I didn't miss anything and it didn't mess up anything either.

If I recall correctly, the command I used was:
setstage SS2C3_MA01 1000

That command will not "force complete" the quest, it just advances it to the next objective as if you had picked up the Stheno. I have also seen a few people mention that for them, the Stheno didn't actually spawn in. This happened to me once before as well. Making sure to save before entering that location could help avoid the missing weapon issue, at least for me reloading my save and entering the area again allowed the weapon to spawn as intended.
This worked like a charm
 
...I sided with the institute but no BOS or any RR came to the meeting.
Are you playing the "vanilla" game, without any quest mods that alter the main storyline or factions?

The "requirements" for each faction to become an ally are listed on the wiki, this page here. Essentially, the main factions (excluding the MM) will require the destruction of the other factions as part of completing the main storyline for that faction. So "siding" with the Institute enough to meet their requirements would prevent you from being able to get either the BoS or RR as allies too.

The quest "Under One Banner" will continue to show even if you have recruited all available allies, and the quest will not be marked as complete until you progress further into the story. I think UOB ends once Call to Arms starts, which is the prep for the final battle. They try to give you enough time to go recruit people until the last minute, but even if you've recruited all possible factions that mission will still be displayed until it ends, if that makes sense.
 
That just means "do more of their quests" so that they'll like you enough to offer an alliance. I don't recall for certain, but you may actually have to reach one of their endings for their alliances to trigger, which means if you reach the ending for the RR, BoS, or Inst then you lock out the other two as potential allies as you'll have wiped them out. If you go for the MM ending and don't antagonize the BoS, you can eventually have the MM, RR, and BoS all as allied factions.
 
The mod mostly wants only one vanilla faction as an ally, and that means others probably destroyed (quest objectives to help others might still be hanging). In my "chapter 3 guide" (link is below) there are some ways to get around it (mostly also involving console, so with all the usual warnings). Some mods may kinda make it make more sense. But it's still us working around the usual vanilla stuff (which SS2 takes into account). So you still can't destroy or piss off a faction forever and ally with them.
 
The mod mostly wants only one vanilla faction as an ally, and that means others probably destroyed (quest objectives to help others might still be hanging). In my "chapter 3 guide" (link is below) there are some ways to get around it (mostly also involving console, so with all the usual warnings). Some mods may kinda make it make more sense. But it's still us working around the usual vanilla stuff (which SS2 takes into account). So you still can't destroy or piss off a faction forever and ally with them.
I like your chart setup but does not work as I think it has been updated.
 
I don't recall for certain, but you may actually have to reach one of their endings for their alliances to trigger...
That is correct. The link I provided in my previous post is to the "Under One Banner" wiki page, which has a section that lists the requirements for each faction to be eligible as an ally. As Torberg mentioned, the MM are one of the "exceptions" with their requirement. The Institute, RR, and BoS require completing the entire main story, which in turn means destroying the other factions (except the MM). But the MM only require you to have completed "Defend the Castle", and not fully destroy the Institute. So if you are mostly siding with the MM, the other factions will still be alive, but the Institute will be hostile.

As Antoine mentioned, his "guide" on Ch3 includes a section for Under One Banner that lists console commands to gain access to factions as allies and bypass SS2's requirements. His guide is a little outdated in some areas due to SS2 updates, such as not listing the Concord faction. But most of the info is still valid, and the listed commands still work. So if you are mainly siding with the MM, and the RR/BoS are still alive, you could try to run their commands to add them as allies. Not sure how nice they'll play around each other during the final battle.

There are some quest mods that allow a "peaceful" ending to the main story, meaning not having to destroy factions and everyone being friendly. But you'll probably need patches or use of certain console commands to make those mods work properly with Ch3. Antoine's guide mentions one of those quest mods, and how to use it with SS2.
 
Well, I just want to finish the story to coin a term overused nowadays. I am ready for the battle with some 60 troopers at the ready. So how do I trigger it?
That depends on your current stage of State of War, and if you have finished any of the other quests that come up during that time. Every once in a while, you'll get to a stage that simply requires you to wait a couple of days for the next stage to trigger.
 
It should maybe be stressed more, but the quests from (a certain individual) such as Outside Assistance, Aide Memoire and everything that follows, are the things that actually push the main story forward. And to get them, state of war objectives must be complete (sometimes maybe an extra random assault to trigger it..)
Other than that, yeah, depends on what stage you're at. Under one banner is kind of a side objective, tutorial quests from holotape are optional.
 
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