I meant when you are in the purifier at the very end of the MQ and you have the option of going into the room and turning on the purifier, giving the code to Sarah, or walking away and not give her the code. If you walk away and don't give Sarah the code will it not allow the Broken Steel quests to happen?
Yes. If you want to continue further in the BS quest line, you must go into the purifier. It doesn't matter what choice you make, but you must still make one, in order for the BS quests to load.