Patrick "Paddy" Doyle, Jr. is an Irish mob boss and Maura Isles' biological father.
Patrick Doyle was raised within a family of thugs from South Boston. His father, Patrick, Sr., his uncles, and grandfather were all members of the Irish mob, so he grew up wanting to be just like them.
Then one day, he met Hope Martin, a Harvard medical student that he fell in love with. Wanting to be good enough for her, he seemed to have tried to get out of the family mob business. They then had Maura when Hope was 18. When his father found out, he threatened to have them all killed. So, given Hope's young age and Paddy's dangerous life, Paddy decided to take matters into his own hands.
One day, he attended Constance Isles's art class at Harvard and posed as a student. He drew a sketch of Hope, grieving at Maura's fake tomb in the Boston Cemetery where he and Hope would sometimes meet, and submitted it to Constance, who tried to encourage him with his art. Months later, he returned to Constance with the newborn, Maura, and asked her to take care of her, telling her that Maura's mother died while giving birth to her.
He then goes on to tell his family and everyone else he knew that Maura had died along with Hope during childbirth. He also leads Hope to believe that Maura had died after her birth, and later leads Maura to believe that Hope gave her up to give Maura her best chance at a life.
In "The Beast in Me", when Maura is performing an autopsy on Colin Doyle, she finds out that Colin is her biological brother. Wanting to know who killed his son, he visits the morgue, posing as a "Mr. Selsi" (Isles spelled backwards). Maura realizes that he may be her father and she tries to get his DNA by offering him a drink, but Paddy straight out offers Maura his blood by cutting his hand. Meanwhile, Jane and the others have by then linked Colin Doyle to Paddy Doyle and later tell Maura.
In "Gone Daddy Gone", a woman named Melissa Black is killed with Paddy's MO and it is assumed by everyone that Paddy killed the woman. However Paddy himself is targeted by an unknown shooter and his number two man, Kevin Brennan is killed in the shootout while Paddy escapes with a bullet wound to the chest. He then travels to his daughter's house with another associate and has Maura perform surgery on him while holding her and Tommy hostage. Paddy then explains that he isn't the one who killed Melissa and begs Maura to believe him based on the other murders he committed. Turns out later that he was telling the truth and the one who killed Melissa and Kevin is a man named Ray Murphy in order to cover up bribery and extortion. Paddy finds Ray first and tortures him for information and the kills him. He then finds the man who hired Ray, Bill Sutton, and tries to kill him too but the police get there just in time to save and arrest him for the murders and putting Melissa's dad into a coma. Later Paddy gives the Black family some money in recognition of their loses and calls his daughter one last time.
In "Burning Down the House", Paddy returns when Maura's life is in danger again when Maura's adoptive mother in run-over and Maura almost is. He reveals that he knew Constance and there was a reason why she chose her as Maura's adoptive mother. He hints that he will find the man who did this and make him pay. When it is revealed that the man who tried to kill Maura is a firefighter named Kevin Flynn, Paddy shows up at a sting operation to bring him in and kills him. He then exchanges fire with the FBI and Boston Police, injuring Agent Dean Porter and is himself wounded when he is shot by Jane.
After being shot by Jane and Agent Dean, Paddy is confined and critical at the hospital. The fact that he is Maura's biological father is now made public. Internal Affairs then begin looking for Paddy's people among the cops, later revealed to be John Connors, Cliff Cummings and Wally Wisniewski. Jane finds his "book" buried under the fake grave he had made for Maura in the Boston Cemetery. After his recovery, he is to be transferred to the maximum security prison Massachusetts Correctional Institution—Cedar Junction, also known as MCI-Walpole.
After IRS investigators shadow Maura and Hope, Jane and Maura realize that Paddy probably was the anonymous donor who funded Hope's medical relief charity MEND which is consequently being investigated for money laundering. Jane, Maura, and Hope visit Paddy in prison asking him to plead guilty so Hope and Maura will be left alone, but he responds "I'd kill for either of you...but I will never plead guilty." When Detective Calvin Ghetts, who investigated the fire that killed Lt. Cavanaugh's wife and child, is murdered, Jane finds out that he had concealed that the fire was arson and that Paddy was responsible. When Maura finds that Hope had bandaged burns Paddy suffered in setting the fire, she gets Hope to agree to testify against him. Paddy later persuades Maura to pick up his newly paroled father Patrick Sr. on his release from prison.
- Sean Cavanaugh's family (accidental)
- Linda Cavanaugh (wife)
- Christopher Kavanaugh (son)
- Fifteen unnamed people
- Thomas "Tommy" O'Rourke
- Ray Murphy
- Bill Sutton (attempted)
- Kevin Flynn
- Sean Cavanaugh (attempted)
Paddy Doyle, despite his status as head of an Irish mob and his infamous kills, lives by a code and is somehow respected by some for it. He only kills men who deserve it: never innocents, children or women. This is later proven false when he is revealed to have killed Lieutenant Sean Cavanuagh's family while targeting him two decades ago (Although this may not count as a violation of his code as there is no indication that he targeted them on purpose).