A young woman named Emily Miller is killed by a shotgun blast while buying flowers in New York City, but Mac is quickly able to determine her death was an accident, the result of a shotgun being tossed off the roof of a nearby building. The intended victim is just two buildings away: Julio Riverton, a family court judge whose badly beaten body was found by his teenage daughter, Madison. Madison tells Mac she'd met her boyfriend Jake and his brother Charlie at the movies and had come back to get money when she came back to find her father dead. A tooth found in Emily's chest matches one broken off from Judge Riverton's mouth and Dr. Hammerback confirms that Riverton died from blunt force trauma. Lindsay tests the shotgun and finds that one of the barrels is faulty and only fires under extreme impact. She also finds red oil based paint on the gun. Stella traces a black sunflower seed used as bird feed to Jonas Stark, a neighbor of Riverton's that the judge was trying to evict, claiming Stark's birds were unclean. Stark denies ever being in the judge's apartment and when she learns Stark dumps the seeds out the window, she realizes one of them must have gotten into Riverton's apartment below through his window. He's cleared when his palm isn't a match to a palm print Hawkes discovered on a napkin by Riverton's body.
Drywall powder on the judge's shirt leads Stella and Angell to Larry Rose, a surly contractor who lost everything in his divorce, a case Riverton presided over. He admits to tracking the judge to his building and grabbing him by the shirt, but left after that to track down his ex-wife, which landed him in jail at the time of the judge's murder. Puzzled by the lack of forced entry, the CSIs turn back to Madison, who Stella learned wanted to live with her mother, not her father, after her parents' divorce. Madison denies killing her father, but when the CSIs go back to examine the evidence, they realize they're looking at a footprint, not a palm print, with the black sunflower seed embedded in it. Lindsay and Hawkes examine the scene again and realize the killer was naked and showered after the murder. The CSIs' suspicion turns to Jake and Charlie when they find traces of popcorn topping on the shower curtain. When they learn the boys have gone from foster family to foster family after Judge Riverton took them away from their father, they know they've found their killers. Charlie and Jake are brought in; they concealed the gun at the movie theater and snuck out to go kill the judge. The older boy, Jake, who wormed his way into Madison's affections, actually committed the murder while Charlie stood by. Mac notes that their crime had five victims: Riverton, Emily Miller, Madison and both of them.
Lindsay asks Flack to track down Danny, who hasn't shown up for his shift at work. She covers for him with Mac, and Flack gets Danny's superintendent to let him into Danny's apartment. He finds a webpage on Danny's computer revealing that Ollie Barnes, who robbed a bodega several weeks ago and inadvertently caused the shooting of Danny's ten-year-old neighbor, Ruben Sandoval, was released on bail. Flack tracks Danny down, and Danny tells him that Ruben's mother Rikki, upon learning about Ollie's release, visited his apartment earlier and stole his gun. Flack agrees to help Danny try to find Ollie before Rikki tracks him down. The pair find Ollie just as Rikki is aiming the gun at him and Danny steps in between them, claiming Ruben's death is his fault. Rikki lowers the gun and allows Danny to take it from her. Flack gets upset with Danny when Danny refuses to arrest Rikki, giving him one hour to bring her in. Danny finally complies and as Angell leads Rikki away, Flack tells Danny he has to stop blaming himself for Ruben's death. Danny sadly replies, "How can I do that?"