An explanation of sorts *Major SPOILERS*
Usually for a mystery/thriller type show, someone already has posted a lengthy and satisfactory summary by the time I get on imdb. But no one has done so for this movie and I think it deserves one, so I thought I'd offer my perspective for all those people going "WTF did I just watch??"
This isn't an easy movie to follow I guess. There are only subtle hints, no obvious answers. We are introduced to John who cross-dresses but assumes his normal personality when he goes to work. But John isn't a cross-dresser, he has no desire to be a woman.. in fact I don't think he has much control over it. We know he's had a traumatic childhood because of the things that his mother did to him. The movie unfortunately did not go into detail there, but it was enough to screw up mind.
I imagine his mother was very controlling and also a big part of his life, so when she died, it triggered a split personality within his fragile mind. This alter-ego Emma(whether that's his mother;s name is not known) wears his mother's old clothes, makes breakfast for John and does the laundry and chores. She even leaves notes for him like mother. It could be that assuming the role of his mother is a way his mind is coping with the death.
All goes fine until a year later when a train crashes into his backyard and his Emma personality captures the attention of the entire town. I think the shock awakened the Emma personality and inspired by Fanny Crill's talk about woman's independence, Emma decides to become more active.
John gets very agitated to find out that Emma has talked to people and made changes to his life. He sees her as his mother trying to take control of his life again, and he believes she is capable of evil. When Maggie and the kid shows up, they have different agendas and a struggle for control occurs. It ends with Emma, the more calm and calculative one faking John's death, so he can't show his face around anymore.
At the end of the show, after Emma takes the snapshot of Jake, it seems like a few posters here think that she had a change of heart. I think that during the flashback his mind went back to the traumatic experience and caused it to switch back to John's. Remember, Emma only faked John's death in the outside world but John is still alive inside, sharing the same space in his/her mind. When he gives Maggie the money and tells her to leave town, he's actually pretending to be Emma just like how Emma was pretending to be John earlier over the phone. This is evident because he says to her "it's not safe here", because he knows its just a matter of time before he suffers another relapse.
I like this movie because it's something different but you really have to fill in the blanks to make it worthwhile.