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.
