-Maura is upset that Jane shot her father believing he was only their to protect her. Jane reminds Maura the Paddy's a mobster suspected in 15 murders. Doyle survives and Maura sits by his bedside at the hospital.
-Jane is under investigation from Internal Affairs for not calling in a BOLO on Doyle and for her relationship with Agent Dean. With their relationship strained, Dean is called back to Washington.
-Jane and the team are called to the murder of a cop during a robbery. They later realize that the cop was dirty and working for Doyle, helping to smuggle guns out of evidence.
-Everyone is looking for Paddy's book that listed all of the people working for him including cops and city officials.
-Jane realizes that an old picture Maura was given by her mother is actually a picture of her biological mother at a gravesit. Jane tracks down a gravestone for a baby who supposedly died, Maura Doyle. Paddy faked his daughter's death to keep her safe and gave her to the Isles to raise. Jane finds the book buried in front of the headstone.
-The book reveals that the Captain is one of the dirty cops. Jane and the team set him up and arrest him.
-Paddy admits to Maura that he would have shot Jane given the chance but things between the two friends are still strained.