Jacob and Margaret decide they are going to let go together, so the show picks up right where it left off during the fall finale. Lucille and Maggie decide to stay home in case Henry returns while Marty, Fred, and Henry go out looking for him.
Margaret tells Jacob the truth about her past and eventually the team finds them and takes Jacob away from Margaret.
Jacob reveals at home that he couldn't disappear because he thought of his parents. Margaret decides that the best thing for her is to be with her kind and be taken away by the government. Margaret tells Fred how a return disappears.
A vaccine has been made, and therefore, Marty will be cured. Marty asks to for the government to let him raise his sister to which they agree to. By the end of the episode, we see a new returned who was the pastor who tried to save Mary when he was baby. He plans on fixing the broken town with Marty's help.
I already don't trust the new pastor and am still holding out that Tom comes back. I hope this isn't the last we see of Margaret, but then again, I don't see Margaret being the "bad guy" anymore and therefore can't add any drama to the story.