Jack Coonan, an enforcer for an Irish mafia group known as the Westies, is found dead in a pool of blood. Jack's brother, Dick Coonan, runs a humanitarian foundation. He figures Jack was killed due to his involvement with the Westies. So, Beckett and Castle head over to the Irish Pub that serves as their headquarters. Westies leader Finn Rourke and his thugs give are less than forthcoming. But when Beckett hears deep groans from a private room, she finds a badly beaten man from a rival gang named Trucho.
Lanie's report indicates that Trucho's nine-inch blade isn't large enough to have caused the stab wounds. Finn Rourke claims that he sent Coonan to find out who was dealing drugs in their part of town. That's a big no-no in this neighborhood. Jack's girlfriend, Molly, tells Beckett and Castle that Jack gave her something to keep safe. It's the key to a bus locker which houses a stack of DVDs by motivational speaker Johnny Vong. The DVD boxes are filled with heroin, giving new meaning to the term "bonus features."
Vong confesses that he teamed up with a heroin trafficker to support his struggling business. The heroin trafficker would bring in his heroin from overseas using Vong's DVD boxes. Fearing for his life, Vong chooses to go to prison rather then give up the heroin trafficker's identity.
Top medical examiner Dr. Clark Murray and Lanie deduce that Coonan's murder must have been by a professional contract killer. Similarities suggest the same person killed five other people. Then Murray reveals some shocking news. He says, "Detective Beckett, there is no doubt in my mind that Jack Coonan was killed by the same man who murdered your mother." Now we know why this episode is titled "Sucker Punch."
This information causes Beckett to doubt her ability to continue with the case. Fortunately, she has Castle to help her through this difficult time. He promises to do anything that she needs including nothing, if that's what Beckett wants. But Beckett says that what she wants is to find her mother's killer. Game on!
Beckett tells Vong she forgot to read him his Miranda Rights, so he's free to go. Vong knows that if he's released, it'll look like he cut a deal. Fearing reprisal, Vong reveals the heroin trafficker is none other than Jack Coonan's brother, Dick Coonan. When Trucho started selling the heroin in the Westies' territory, Rourke sent Jack to investigate. Vong adds that Dick sent a hired killer after Jack, an assassin known as Rathborne. This is the man who murdered Beckett's mom.
Dick Coonan realizes that Beckett is emotionally invested in this case. He swings a deal for immunity and will set up a fake contract on Vong's head to lure in Rathborne. Coonan says the $100,000 upfront fee is a small price to pay to catch her killer. Unfortunately, the city won't pay that much, but Castle will. He did say he would do anything she needed, right?
The trap is set, but the contract killer never shows. Beckett beats herself up over the failed plan until she realizes that Dick Coonan told her the hundred grand would help catch "her" killer. Beckett never told Dick that it was her mother that Rathborne had killed. That means Dick Coonan IS Rathborne!
Beckett rushes to confront Dick Coonan in the precinct, but before she can act, he steals a cop's gun and jams it into Castle's back. Montgomery draws his gun, but Beckett needs Dick Coonan alive to catch the people who hired him to murder her mother. Castle knocks his head back into Dick's face to free himself. But the killer recovers quickly and takes aim at him. BANG! Beckett fires. Coonan is down. To save Castle's life, Beckett has killed the only link to solving her mother's murder.
Afterwards, Castle apologizes for having forced Beckett's hand. He tells her he's done doing the police thing. Beckett says, "If you tell anyone what I'm about to say, there's going to be another shooting, but...I've gotten used to you pulling my pigtails. I have a hard job, Castle, and having you around makes it a little more fun." Castle smiles and says, "Your secret's safe with me." Sorry, you two, but that's not the world's most well-kept secret.