The Institute

The Institute is likely the descendant of the Massachussets Institute of Technology, located within the Commonwealth. Little is known about Institute other than that the scientists working in the sealed environment of the institute possess highly advanced technology and technological skills. The Institute has created true AI and is capable of creating convincing androids.

Another organization active in the Commonwealth, the Railroad, functions in direct opposition to the Institute, as their goal is to free sentient androids from their creators.

Contrary to fierce arguments from The Railroad, there is not much evidence provided to demonstrate that they are either "good" or "evil"; in The Replicated Man, Dr. Zimmer simply wants to safely recover his creation, and when aided in this, he lectures the android on the advantages of staying in the Commonwealth, and leads him unharmed (or simply reset) out of Rivet City.

Connection to the Enclave
There is a lot of debate as to whether or not the Institute has a connection to the Enclave, the center point of this debate being the origin's of Harkness's A3-21's Plasma Rifle (Something only obtainable one way or another through the Enclave), and the technological/production capabilities of the institute in general. (Being that they can produce androids (something that even the Capital Wasteland Brotherhood of Steel Scribes deny as little more than a fantasy) and in such large numbers that runaways are apparently a frequent problem.)

Officially, there has been no word whatsoever either denying or confirming this theory.

Appearances
The Institute only appears in Fallout 3.