|Occupation||Police officer (retired)|
|Family|| Peggy Brannigan (wife)|
J.J. Brannigan (son)
In 1981, he worked as the commanding officer in the Marybeth Mosley rape-murder investigation. He initially suspected a plumber named Fred Jenks until he found a new suspect in Michael Sarno when he takes a witness statement from Janice Trainor.
Brannigan's boss, Alvin Holsick, was in the pocket of Michael's father Peter. He forced Tommy to stop investigating Michael and offered Tommy a promotion top First Grade Detective if he did. He accepted the bribe, helped Holsick's driver steal the evidence from property lockup, and destroyed Janice's statement. When Detective Charlie Curran tried to investigate Michael, Tommy blocked him and eventually Alvin had him demoted to Officer.
In 2000, Brannigan's old subordinate and partner, Lennie Briscoe, reopens the case and asks him for background. He points the finger back at the plumber, but as they continue the investigation, they discover a car connected to Michael and start to suspect him. Brannigan brings his son to the station as Briscoe informs him of the arrest of Michael. He asks if they intend to call him as a witness and Briscoe doubts it and Brannigan leaves.
After ADA Carmichael discovers Holsick's involvement in the cover-up, they start to suspect Brannigan of helping. McCoy and Carmichael call Brannigan to their office. There, they ask him directly if he covered up the murder and Brannigan deflects their questions. He is later called to the stand as a defense witness where the opposing counsel has him bring in the other suspect in the case to cast reasonable doubt. On cross-examination, McCoy gets Brannigan to confess he took a bribe to cover up Michael's involvement in the murder. Michael eventually takes a plea for manslaughter in the second-degree. Briscoe later visits him at his house and Brannigan tells his ex-partner how he regrets his part in letting a murderer go. Brannigan asks if he forgives him for and Lennie says he does.