Due to a lack of funding for the US Marhsalls, Van Pelt is assigned to a witness protection duty, alternating shifts with Marhsall Vic Gorman. But when she chases a masked intruder off into the darkness, someone else in the house kills Derrick DeGeorge, the man she was supposed to be guarding. The rest of the CBI team is called in, and Jane finds Derrick's 13-year-old daughter Trina hiding in a treehouse. Both her parents are now dead, causing Jane to bond with the young girl.
The investigation starts with drug dealer Sean Essex. Derrick saw him commit murder, and was going to testify against him - that was why he was in the witness protection program to begin with. While Sean admits that he has no alibi for the previous night, Cho cuffs him and drags him outside. That's when his ankle monitor goes off. How could he commit murder while under house arrest? Later, when questioning one of his lieutenants, the agents learn that he was able to set his cell phone to the same frequency in order to escape. He flees custody and immediately becomes suspect number one.
Meanwhile, LaRoche approaches Van Pelt and tells her that if she agrees to help his investigation, he will smooth over the fact that she let a witness die on her watch. Otherwise, her career path might not be so smooth. She is conflicted - the last thing she wants to do is turn snitch on her own department. She asks Rigsby and O'Laughlin for advice, but never quite comes to grips with a decision.
When Van Pelt and Rigsby capture Essex, they put Trina in front of a line-up in the hopes that she will ID her father's killer. While she doesn't ID anyone, Jane later announces that he (falsely) hypnotized her and she now remembers everything. The CBI pretends to take her to a safe house...where Marshall Gorman shows up to kill her. Luckily, Jane, Van Pelt, and Lisbon are waiting for him. A gunfight breaks out, and Van Pelt kills the assailant. Turns out, he was on Essex's payroll. Jane figured out that he and Essex grew up together on the same block in Boston, and they've been working together since the beginning.
After the fight, Jane and Lisbon approach Trina alone. Jane tells her that he alone knows the truth: she discovered her that her father killed her mother, and killed him in a struggle after confronting him. Gorman did try to kill Derrick, but he was the intruder that Van Pelt scared away. When Trina admits the truth, Jane and Lisbon have a major fight over whether or not to turn her in. In the end, Jane gets Lisbon to reluctantly agree to let Trina go free with her aunt.