The blue flu sweeps the NYPD following a pay dispute for officers, resulting in 40% of the force calling in sick. Mac Taylor, on his way to a charity function for the Manhattan Museum Restoration, notes the lack of cops on the street and at the precinct when he stops a shooter himself. Stella is at the function with fireman Brendon Walsh as her date. The two watch wealthy newspaper publisher Robert Dunbrook unveil a million dollar donation to Deputy Mayor Stuart Kaplan's charity, but when he calls for Kaplan to accept the check, the man doesn't appear. The reason is quickly revealed: a multitude of balloons are released from above, and with them; the body of the deputy mayor.
Hawkes and Danny arrive at the scene, but Danny quickly pleads illness and, despite Hawkes' scorn and skepticism, leaves the scene. Stella finds a circular trace pattern of blood on the floor and thinks that the origin of it might lie with Brendon, who rushed to help Kaplan after his body landed. She goes off to collect his clothes, leaving Hawkes and Adam to process the scene.
Neal Weston, Kaplan's brother-in-law comes looking for Kaplan's thirteen-year-old son, Jake. Adam searches for the boy and finds him hiding in a cabinet. He's able to draw him out with the offer of a soda and the use of his iPod. Stella tracks Brendon down and retrieves his clothes.
At the morgue, Sid determines Kaplan was strangled, noting an odd bruise pattern on the side of his neck, possibly made by the murder weapon. The team gets a lead when Hawkes finds a broken off part of an NYPD badge belonging to a detective named Stan Miller at the scene. Mac questions Miller, who admits to confronting the deputy mayor over the pay cuts and confesses they got into physical fight, but insists he left Kaplan alive.
Hawkes is irritated when he gets a call to fill in for Danny on a court case and expresses his frustration to Lindsay, who defends Danny. Stella recovers a small bloody wood chip from Brendon's clothes, while Lindsay discovers several hairs on his body came from a horse.
Deputy Inspector Gillian Whitford pays Mac a visit: someone left a copy of The Ledger, Dunbrook's paper, on her windshield after the gala with the words "Follow the money" written over Kaplan's picture on the front page. Gillian is determined to get her hands on Kaplan's financial records, and Mac points out that before being named Deputy Mayor, Kaplan was the Commissioner for Construction and Renovation.
Adam matches eyelashes on the balloons Kaplan fell with to his son, Jake, and he and Stella posit that the boy is likely OCD. Because the transfer occurred right around the time of death, Stella wonders if Jake killed his father. Despite Adam's skepticism, Stella notes that the boy could have strangled his father by applying pressure to the right places.
Lindsay offers up another lead: the horse hairs on Kaplan's body belong to a thoroughbred owned by Robert Dunbrook. Mac questions the man, but Dunbrook tells the CSI that he ran into Kaplan in the bathroom and urged the man to put their differences aside, patting him on the shoulder as they walked out. Mac is skeptical; Kaplan was a roadblock for the powerful Dunbrook.
Lindsay IDs the wood from the chip as balsa wood, but she and Stella are interrupted when a chagrined Hawkes calls and tells Stella that the case Danny was supposed to testify at was thrown out because Hawkes was railroaded by the defense. An angry Stella goes to confront Danny at home, but when she gets to his apartment, she has calmed down and can understand his point of view -- even if she doesn't choose to make the same stand.
Gillian brings evidence against Kaplan to Mac: the deputy mayor was running fraudulent charities. Mac points out that the person who left the newspaper on her car left it two hours before it was published, leading him to suspect it could have been Dunbrook.
Adam finds trace on his iPod and is surprised when it matches trace found on Kaplan's neck, linking Jake to the murder. Stella is finally able to identify the bruise on Kaplan's neck as one made by a clip on tie. Stella and Flack go to Weston's house to find Jake, and Stella spots a board game with pieces like the one found on Kaplan's body. Flack recognizes the boy as the same one who he saw sitting in the precinct earlier, waiting for Adam.
Stella and Mac try questioning Jake to no avail, so they turn the boy over to Adam. Adam recognizes OCD traits in Jake, and draws the boy out. Jake tells Adam that his father found him hiding during the party and snatched away the game piece he was holding. Jake lost control and attacked his father in order to get it back, accidentally killing him in the process. Jake tells Adam that even though his dad was mean sometimes, he really loved him.
Adam leaves the precinct upset, followed by Stella, who is concerned about him. Mac gets a call to meet Dunbrook and is surprised when the man opts to end the union stand off by handing Mac a check for twenty million dollars for the NYPD. Though Mac has qualms about taking the check, Gillian does not. Danny returns to work, and immediately offers to help Hawkes with his workload.