When a woman and a young boy are murdered in a house, CSI processes the scene, but they get a special visitor from the FBI: Jack Malone. Malone flew in because there was a hit on VICAP to a palm print found in the house that echoes a NY kidnapping case six years back. An adopted boy was taken from his home and his babysitter was murdered. He's been missing ever since.
Evidence from the house leads to a poker player from Utah; his son and his ex-girlfriend were the vics in this case. He wasn't involved in their deaths. But DNA from the woman's body matches that of two other rape-murders in CODIS; one in Wyoming and the other in Idaho. A short time later, another rape-murder turns up, this time with the victim's husband killed as well. Sara takes the case hard; the constant bad news is getting to her.
Grissom and Malone realize that the killer is riding the freight train to various points, then hopping off and killing innocent people as he likes. They track him to a casino, only to find he's abducted a woman and killed a police officer as he fled the area. Later they find that the man, Terry Wicker, has also taken a young boy from a local school. When they come across the vehicle the man was driving, they find the missing woman in the trunk and ID her as Wicker's ex-wife, and the mother of the boy Wicker has taken. It's appears that the man came back to find his son, and perhaps take revenge on his ex.
Meanwhile, Wicker leaves town on a bus, with his son beside him.