A little 10 year old girl named Rachel Barnes arrives home from a sleepover at a neighbor's place, to find her mother Dr. Valerie Barnes dead of a gunshot wound to the back.
Valerie was a therapist at a counseling centre in Richmond. Her husband Commander Ryan Barnes was in survival training when she was shot.
Ryan's name and picture was posted to a jihadist website hit list after personnel details about a military op were leaked.
Thinking that Valerie's murder had something to do with the jihadist information, Abby, Bishop and McGee come up with a plan to contact the website's owner, Dorian Hobart, a man who had been dishonorably discharged from the army, and who then had become involved with several anti-government extremist groups.
McGee poses as an electronics expert who specializes in detonators. He meets Hobart at a park, where McGee hands over a sample of his work. Just as McGee gets set to arrest him, he is tackled to the ground by a woman who turns out to be ATF Special Agent Zoe Keates, an old Philadelphia PD partner to Tony.
It turns out that the man McGee was dealing with isn't Hobart - he is another ATF agent posing as Hobart. The two teams had stung each other.
After Ducky finds out that Valerie had an old facial injury for which there was no medical record, Tony does some digging and discovers that she had been severely injured while working as a forensic psychiatrist in Maryland. One of the prisoners had gone berserk during his pre-trial evaluation and had injured her. The prisoner was a serial killer and cannibal named George Burton. The team finds out that Valerie had paid him a closed-door visit two weeks prior to her death.
Upon interviewing Burton, Tony and Gibbs find out that she had sought his advice about another unnamed sociopath - one who scared her more than he did.
Abby pieces together the fragmented bullet that had killed Valerie, and ties it to a ballistics report about a gun that had misfired. There was no injury involved and therefore no charges were laid. The gun belongs to Nathan Curtis - the man who had hosted the sleepover that Rachel had attended.
Curtis tells Gibbs and McGee that he knew something was wrong between Ryan and Valerie: he saw that she was on edge every time Ryan was around Rachel. When Curtis saw bruises on Rachel, he had confronted Valerie, but didn't report his findings to anyone because she told him that Ryan would never hurt his daughter.
Suspecting Ryan may be the killer, Tony and Bishop go to his hotel, only to find that he and Rachel had never been in their hotel room.
The team pings Rachel's phone and discovers that she and her father were in a park. They go there and arrest him, upon which he confesses to killing his wife.
Meanwhile, Ducky uncovers some medical reports about Rachel, who had suffered broken bones, two concussions and multiple lacerations - all of which happened when Ryan was deployed overseas.
Gibbs interviews Rachel and shows her the gun he'd found beneath her backyard fort. She confesses to her whole scheme: that she had injured herself repeatedly so that her father would come home. While he would come home sometimes, he never stayed long enough for her liking. She figured he would come home to stay if her mother was gone, which is why she killed her. While at the sleepover at her neighbor's house, she snuck out long enough to kill her mother and then got back before anyone knew she'd been gone.