When the odds seemed to have been stacked against him somehow fate found a way to save Dexter. Of course in this case fate has a name: Lila.
So she steals his GPS out of his car, goes down to the everglades and discovers Doakes locked up. Doakes tells her that Dexter is indeed the Bay Harbor Butcher. However Lila, instead of helping Doakes escape, helps Dexter in burning the entire cabin down with Doakes inside. Lila sympathizes with Dexter. This is the dark secret that he has been keeping this entire time. He feels alone. She feels alone. They're soul mates, right?
Well with Lila knowing this, and her definite need to keep some sense of emotional stability, she uses this opportunity to get Dexter to supposedly play right into her hands. And the only way to do that is to attack her competition somehow. To attack Rita.
And even though Doakes being killed by fire is not how Dexter would've wanted it to play out, it helps him nonetheless. He wasn't there. He has an alibi. The Bay Harbor Butcher case is now coming to a close. However this sense of contentment is short-lived when he discovers not only his burned out GPS in the collected evidence, but also that the cabin burning down wasn't an accident at all. And when Dex discovers that Rita's kids are kidnapped, everything points to one person. It's the one final loose end in his life. Lila. Dexter has to take care of that himself, and learn that disclosing and trusting too much in one person is the most dangerous thing he can do.
It seems that Batista is going to be absolved for the rape that Lila put on him. Laguerta is of course completely shaken up by the loss of Doakes, and still believes he's innocent.
And with them closing the books on the Butcher, Lundy has been reassigned to Portland to work another serial killer case. Deb wants to come with him, but at the last minute she has to make a choice between helping her brother find Rita's kids, or run away with Lundy.
In the end the season closes the only way it could, with Dexter killing his main antagonist. Lila loved Dexter, but wanted too much from him. What does Dexter want now? A new start. And this new beginning starts with the end of her.