Upon Elizabeth's return to Columbia, she witnesses a meeting between Fitzroy and the Lutece twins just minutes before the revolutionary's death. At this point, Fitzroy has captured Fink and his son. The Luteces explain to Fitzroy that it's crucial for Elizabeth to become a woman and gain the strength to kill Comstock. In order for this to happen, Fitzroy needs to force Elizabeth into the proper mindset. At first Fitzroy refuses to harm Fink's son, saying that, although she wants to see Fink and Comstock fall, the sins of the father should not be taken out on the boy. The Luteces hint that she doesn't have to kill him, but to just threaten him enough so that Elizabeth will have no choice but to "mature" into a killer. Fitzroy is saddened that she will not be able to survive the revolution, but she accepts that she must die if it means that it will lead to Comstock's death as well. This turns Elizabeth's opinion of her from a psychopath who is just as bad as Comstock to a martyr willing to give the ultimate sacrifice to her cause.
Interestingly enough, the revolutionary character gets vindicated in a way that is just as convoluted as the setup to make her look bad: