So I find out Shaun is "Father" in charge of The Institute and he asks me to join them. The first question I would ask is what are the institutes goals and what are they hoping to achieve?Now at this current time all the player character knows is that the institute is feared, and for some reason have been kidnapping and replacing humans on the surface. Why... do they hope to replace the human population with synths? I am guessing not because from what I gather the institute does not see them as anything more than machines. I don't understand why you are not given the opportunity to ask Shaun what they do. Perhaps I am being thick or have missed some information somewhere that explains it all. Can somebody please enlighten me...

Go talk to the rest of the institute employees and talk to Father a bit more, the more people you talk to the better of an idea you'll have

I have talked to all the people that you are asked to talk to, and I am still not really any the wiser. I get the impression that they want to use synths as some kind of law enforcement to create a new civilization above ground, but what kind of civilization? Why are they kidnapping/killing people and replacing them, as some kind of covert information gathering? Why go to that extreme? Why not if they are indistinguishable from everyone else just send up synths to gather info without kidnapping and replacing them? I just don't get it and I am not sure I have even got any of that right? Surely I should just be able to ask Shaun what is going on? None of it is really making much sense to me?

The Institute is a underground Vault-like nation of scientists which wishes to continue existing and conducting their experiments in peace. They do not intend to replace humans with Synths because they consider Synths not to be human or sentient. They, instead, fear the surface world a great deal and believe (correctly) that parties involved want to wipe them out (The Railroad, the Brotherhood of Steel) so they use Synths to infiltrate and spy on the Commonwealth.

They don't seem to realize how paranoid this has made the Commonwealth about them or how angry. Also, several scientists have been experimenting on Wastelanders in ways which is approved by the leadership but not by the Institute at large.

The Institute's primary goal is to continue to exist in their safe, secure, 1st World Lifestyle.