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I've read other questions here about this, like this one and I'm still unclear about something. Some answers suggest that you can get the help of all the factions at this point to continue their quest lines.

But when I speak with one faction, it disables speaking with the others. The quest markers go away, and speaking with the other faction leaders doesn't give any dialogue about the teleporter plans. If I buy the plans back from Tinker Tom, for example, it DOES give me the quest objectives again, but they still wont talk to me.

From reading about it, your chosen helper will show up at the build site to help out, and it might be a bit awkward for all three to show up.

So is there an option to continue the faction quest lines (up to the point where you'll alienate one) from here? If I go the loner route and build it myself, will I be able to do the quests like getting Dr. Li to join the Brotherhood, Liberty Reprimed, etc?

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Although you can mix and match quest lines and switch faction affiliations at various points in the game, you have to pick one faction to help you build and operate the molecular relay.

This will be one of the Railroad, the Brotherhood of Steel, or the Minutemen. Having the Minutemen aid you could easily be referred to as "doing it yourself" since at that point you're the leader of the Minutemen, and they would be acting on your orders.

To be clear, you can have only one faction help you build the relay, but can still switch which faction you ultimately support later. If you've already completed the faction quests with each other faction up to the point where you could have asked them to help you build the interceptor, then you should be able to continue those questlines with them regardless of who actually helps you build it. If you haven't been doing quests with the faction up to this point, then you might get locked out.

For more details on this quest and the steps needed for completion with each faction, refer to the The Molecular Level page on Nukapedia. Official guides often contain errors, but errors on the wiki are usually fixed, due to the fact that it's a wiki.

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  • I know you can change affiliation, but my question was whether any major quests get locked out if you don't pick the faction that give those quests-- the linked question seemed to suggest that it would. – travisnewman Dec 9 '15 at 2:15
  • @travisnewman I think the quest with the network scanner holotape will probably get locked out, and maybe a couple others, but I can't actually say for certain. Looking at those quest pages on the wiki, it sounds like you might be able to take the holotape to each expert afterward. Not sure. – DCShannon Dec 9 '15 at 2:27
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This is not a complete answer, but I've answered my own question to a point.

I couldn't get the option to build it myself. The official guide mentions that path, as well as a few other guides, but it would never work for me. I went with the Railroad, then after Institutionalized I traveled to the Prydwen and spoke with Maxson who chewed me out for not building the device with the Brotherhood, but then gave me the quests that would have come at the end of Molecular if I'd gone with them.

However, Inside Job still isn't triggering. I have the tape but I can't get Sturges to look at it.

So, as I said, this is a partial answer. A complete one would still be nice if anyone has a way!

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  • Making it "yourself" is making it with the Minutemen. Have you been doing Minutement quests? What's the last one you completed? Did you take the Castle? – DCShannon Dec 8 '15 at 20:49
  • @DCShannon I was of the understanding that there was an option for the Minutemen, and then there was making it yourself (if you had the plans). This may be incorrect, but I'm curious - where have you got the link between yourself and the minutemen? – Jeeva Dec 8 '15 at 22:36
  • @Jeeva You're the general of the Minutemen. Them doing things is you doing things. You need a technical expert to look at and interpret the theoretical plans to turn them into engineering blueprints, so you can't take the plans and build it without help. Sturges is your expert. – DCShannon Dec 8 '15 at 22:41
  • @DCShannon From everything I'm reading there's four options. Minutemen, Railroad, Brotherhood, and neither. The official guide, various walkthroughs online, and anecdotal accounts confirm it's possible. You just skip talking to anyone and just build it from the workshop. But plenty of people are missing that option. – travisnewman Dec 9 '15 at 1:38
  • And "You're the general of the Minutemen" and "Sturges is your expert" aren't necessarily true, depending on where you are in their quests. Here's a screenshot of the official guide. Method 1 is the Minutemen. Method 4 is on your own: i.imgur.com/RsQ3vRp.png – travisnewman Dec 9 '15 at 1:44
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Yes, note that in the quest log that speaking to the three factions are all optional components of the quest.

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