A father is taking his son to a Yankees game as an 11th birthday present. They get separated at the train station, and the son disappears. The next morning, the Missing Persons Squad is called into the case. Bob, the father, claims his son Gabe is not having any problems, and would have no reason to run away.
After his stunt in the last case, Martin is assigned office duty, and told to check all the sightings and phone calls. As the checking goes, they find a scalper who bought and sold Gabe's ticket. The kid must have used the money to go somewhere.
At school, his teacher tells the squad Gabe reacted strangely to the Happy Birthday song and cake his colleagues tried to offer him. Still appalled Gabe's run away, his mother admits he might be upset about his new baby sister and their moving – they've moved just six months before.
A skateboard found in Gabe's room leads Jack and Danny to some place on the West Side with loading docks where kids go skateboarding. A teenager there tells them Gabe had been there the day he disappeared, and had left with everybody else around 9 pm.
A call to the Bureau leads the squad to Port Authority – but they only find Gabe's jacket, with blood on the sleeve. The boy wearing it swears he found it in the garbage. Jack goes back to the parents' to get samples for a DNA test. Danny looks for the youngster who told them about Gabe's arrival at the loading docks. This kid, Wally, eventually admits Gabe left with some guys who were going to "mess up with some Koreans".
Samantha investigates a cybercafé near Port Authority where Gabe was also seen. Martin discovers the Korean deli owner the kid was talking about and Danny goes talk to him. The deli owner tells Danny Gabe had been there with a bunch of others; he tried to lift some snacks, the shop owner grabbed him and he struggled. When they fell, the Korean hurt his head and passed out. Gabe must have thought he had killed the man.
At Port Authority, Vivian learns Gabe tried to buy a ticket to Texas. The email he sent from the cybercafé asking for help was addressed to "Dad" – what brings the suspicion right back to the parents. "If he was in trouble, why didn't he come to us", wonders the mother. "He did", Jack states. "He sent an email to his father." Bob denies is vehemently, and his wife suddenly understands. Gabe found his biological father – he's adopted, a small detail the parents had failed to tell the FBI.
As it turns out, Gabe's biological father has died three years before. He was talking to someone else – someone who lives in Texas, and is probably a pedophile. Tracking child tickets bought that night, they find Gabe – in Santa Fe. Intercepting a message exchange between the boy and "Dad", they learn they are meeting at a park in Santa Fe. Jack flies there with Danny and Martin – his good work on the case got him "out of the doghouse" and back in the field. They set up a trap at Gabe and "Dad"'s meeting place. When the pedophile tries to run, Martin tackles him into the lake. Gabe is safely returned to his parents. Case closed.