The Commonwealth itself is nothing but a war-ravaged quagmire of violence and despair. Inside the sealed environment of the Institute, however... But... the Institute's affairs are none of your concern. Your undeveloped mind couldn't even begin to comprehend what we've accomplished.
The Institute existed long before the Great War, but was originally known as the Massachusetts Institute of Technology (MIT). It is known that Robert House attended the Institute in his youth. After the Great War, the Massachusetts Institute of Technology survived, but became known to the people of the wasteland as a secretive organization known only as the Institute. Allegedly, it is currently located within the Commonwealth, the name now given in the post-atomic world to what was once the American state of Massachusetts. Little is known about the Institute aside from rumors circulating around the scientists working in the sealed environment. The Institute possesses highly advanced technology and technological skills, resulting in the creation of true artificial intelligence (AI), and are capable of creating androids.
In Fallout 3's Broken Steeladd-on, it is mentioned that Dr. Madison Li supposedly went north to visit the Commonwealth, where the Institute is located, after the events of Take it Back!. Whether this was truly her intention and whether she actually made it there is currently unknown.