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The Institute would get blown up, and if I left things in there, are they gone forever, or are they teleported to one of my settlements?

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When the Institute becomes inaccessible, everything in it will unfortunately be lost forever. So don't stash anything of value in there, unless you plan to finish the game on the Institute route.

  • This is basically true, but the other faction quest lines eventually result in an assault on the Institute. I can't recall if there's a way to get to your room and loot the containers at that point. – DCShannon Jan 17 '17 at 20:16
  • @DCShannon I don't think so. There are a lot of closed doors in the Institute atrium during the assault which block most of its areas. – Philipp Jan 30 '17 at 19:47

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