Finishing the main story first?

[Hephalumph]

I am sure it has been done, and discussed; but I can't find any such discussions either here or on Reddit, so I thought I would just ask... what happens to the SS2 (chapter 1, and/or 2) storyline if you don't even begin it until after you completely finish the main quest? Not starting it on an old character, let's say I start a new save from scratch, but just never start settlement building / SS2 until after I have found Shawn and blown up (or, I guess if you prefer, joined/become the leader of) the Institute?

 

[Cessori]

I've not played through SS2 having completed the vanilla story to the end. Probably will be fine, just some of the NPC dialogue might not quite be right for that situation. I know some have lines for that possibility.

 

[lordoftheapes79]

I did a perfect Minuteman ending last month, so starting the SS2 story was unavoidable. Overall, it's written to stand beside the MSQ without interfering, so mostly there are just side comments, BUT when you get to THAT part of chapter two, your options are dependent on which factions you're on good terms with. So there's a bit of variation depending on where you are in the MSQ and what choices you've made.

 

[yaugie]

Something to note that's kind of sort of probably a spoiler for Chapter 3: There's an NPC added inside The Institute by Chapter 2 that doesn't presently do anything. This particular NPC may become relevant later. (when I asked about them, Sirick only gave a :D in response)
No idea what that might mean for people who'd already blown the place up by the time they reach that point in SS2's storyline.

 

[lordoftheapes79]

Something to note that's kind of sort of probably a spoiler for Chapter 3: There's an NPC added inside The Institute by Chapter 2 that doesn't presently do anything. This particular NPC may become relevant later. (when I asked about them, Sirick only gave a :D in response)
No idea what that might mean for people who'd already blown the place up by the time they reach that point in SS2's storyline.

I'm personally pretty confident in Sirick's ability to set up contingencies at this point, but given we know we're getting Conqueror gameplay with integrated factions, he's likely the institute contact for this. So, if you blew up the institute already, it doesn't matter, but if I'm wrong, I really hope you issued the evacuation order....