Contains Spoilers

Right i am doing the end of the line quest and it says i have to kill the railroad leader. Instead of killing her i warned her. Now on the underground undercover mission i am stuck on the bit continue working with father.

How can i continue?

Despite well over 250 hours I have never done that quest. But if you have not read the wiki; then I give you http://fallout.wikia.com/wiki/Underground_Undercover - Beware that it does contain spoilers if you scroll too fast but could none-the-less prove useful or useless.