You will learn that he is actually Shaun and that time has passed many years since you saw him taken. After some dialogue with him, the mysterious Father will come in to speak with you. The elevator will stop, and you will step out to find a room with a small boy who turns out to be a synth version of Shaun. You will get your first glimpse of the Institute’s operations as you move down. You will see an elevator ahead of you which will take you to him. He will invite you to come and meet with him.
Once inside, you will walk out of the relay room to hear a voice on the intercom system. If you want to join the Institute, then it doesn’t matter what faction you work with to build the teleporter.
In this quest, you will be tasked with building a teleporter and entering the Institute. As you progress through the main story and the questlines of other factions, you will eventually get to the quest “ The Molecular Level”. You will likely hear of the mysterious Institute as you interact with others in the Commonwealth. The Institute’s general practices often cause harm to the people of the Commonwealth. Those who believe in synth rights, like The Railroad, are opposed to the Institute due to their enslavement of synths. Those afraid of synths believe the Institute’s creations are dooming what’s left of humanity. Virtually everyone in the Commonwealth has problems with the Institute. The Gen 1 and Gen 2 synths were easy to identify as synths, but the Gen 3 synths created using Shaun’s DNA were indistinguishable from humans. Shaun was useful because he had been preserved since before the war, therefore his DNA had not been exposed to radiation. They used Shaun’s DNA to perfect the human side of the synths. The Institute are directly tied to the Lone Wanderer, as they kidnapped their son from Vault 111 while the inhabitants were kept in cryogenic states. Fears of the Institute were vindicated when the Institute sent a synth to ambush a meeting between the various Commonwealth groups, and they have essentially been enemies since. While the Institute’s vision was positive, they were willing to use any means necessary to achieve their vision. However, there were fears about their true intentions, and people were afraid of the synths that they were building.
They initially intended to work with everyone else in the Commonwealth. They aimed to continue advancing technology to help rebuild the Commonwealth. It was largely founded by scientists from the CIT who survived the war. The Institute headquarters is located under the ruins of the Commonwealth Institute of Technology, or CIT. (There will be massive spoilers for the Institute in this guide). Until you meet them personally, you will only find out tidbits of information and hear the fears of them from others in the Commonwealth. The Institute is usually the last faction you will meet in Fallout 4.
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