When you set the 3 proton bombs, and you need to find the codes to get the last one out of the missle thing- where or how do you get them?

There's a computer terminal in that same room. I forget exactly what you do but you disable something from there and it will then allow you to get the proton core.

Yes as Ladrummer said it's proton CORE, so make sure that your looking for the right thing or you may miss it , and all you have to do is go to the terminal in the same room and hit all the available options then "use" the missile.