I'm confused at this point because of the underground undercover mission.. After I met Z1-14, I have to go warn Desdemona that the brotherhood of steel discovered the location of the railroad hq. Thing is, when I fast travel to the railroad hq to go warn Desdemona, the railroad are all of a sudden hostile. I'm stuck now. How am I going to finish the game now on the railroad's side if they're all hostile? Is there an explanation? I also have another mission to do for father that's called end of the line. I'm so confused at this point :S

Sounds like a bug to me. Try not to fast travel to Railroad HQ but instead travel to somewhere nearby and go there by foot.

So - I take it you have read the Wiki description of this quest?
http://fallout.wikia.com/wiki/Underground_Undercover
As you can see, it can go sour several different ways and can be Failed.
Maybe read the Wiki info carefully (or even print it), load your save and try again?