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Where Does Shaun Go After You Destroy the Institute in Fallout 4?

Taking synth Shaun during The Nuclear Option sends him to the Castle with the Minutemen or the Prydwen with the Brotherhood. Leaving him behind has him die in the explosion, except on the Railroad route.
WorldFallout 4? Length2 min Posted Quest giverVGSources Team

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If you take synth Shaun with you during The Nuclear Option, he goes to the headquarters of the faction that destroys the Institute. With the Minutemen he is at the Castle, and with the Brotherhood of Steel he is aboard the Prydwen. If you leave him behind, he stays in the Institute and dies in the nuclear explosion, except on the Railroad route, where Tinker Tom says he will teleport Shaun out and arrange his care.

Which Shaun this covers

This article is about the child synth Shaun, designation S9-23, who was created by the original Shaun (Father). It is not about the original Shaun. The choice of whether to take him or leave him happens during The Nuclear Option, the faction quest in which you destroy the Institute.

Where he goes if you take him

The faction you side with determines his destination. The table below reflects the locations given in current quest reference documentation for Fallout 4.

Faction that completes The Nuclear Option If you take Shaun If you leave Shaun behind
Minutemen Castle He dies in the Institute explosion
Brotherhood of Steel Prydwen He dies in the Institute explosion
Railroad Railroad headquarters is listed as an optional location for him; the reference documentation does not give a further detail for this outcome Tinker Tom says he will teleport Shaun out and arrange his care; he does not appear again in the game after that dialogue

What happens if you leave him behind

Leaving Shaun behind removes him from the rest of the game in every route. The outcome differs by faction only in how he exits the story.

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Minutemen and Brotherhood of Steel routes

Shaun stays in the Institute when it is destroyed and dies in the explosion. You will not see him again, and you will not get any of his later interactions.

Railroad route

Tinker Tom offers to take Shaun out of the Institute before the blast. The dialogue says he will teleport Shaun to safety and arrange his care. The game does not show Shaun again after that conversation, so the player never learns where he ends up.

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What taking him changes later

If Shaun comes with you, he remains available for item-gathering and crafting interactions after the Institute is gone. These include the Wazer Wifle. Those interactions are the only later payoff tied to his survival, so the choice matters for players who want them and matters little otherwise.

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