Stephanie McNamara, a.k.a. The Ghost Killer, was a prolific serial killer who had remained under the radar for decades.
In this episode, a serial killer named Christopher Pelant reveals to Brennan that there is another serial killer still at large. Pelant may or may not know them personally, but he has "a reason to believe it's a woman." Through this episode Pelant leads Brennan to six of her victims and tries to get Brennan to investigate, but Pelant is killed, leaving the Ghost Killer still at large.
Pelant: These people were killed in different geographical locations, killed by completely different methods, different ages. Nothing to connect them, and yet, they were all killed by one person.
Brennan has nightmares about Pelant and his possible companion the Ghost Killer, becoming rather obsessed with the thought of another serial killer. When another victim is supposedly discovered Cam reassigns the case to Clark Edison so there is an objective eye. It is revealed that the victim's death was covered by a corrupt medical examiner named Leslie Dollinger who died years later and the evidence points to Hodgins' old friend Trent McNamara. When Trent supposedly commits suicide, Brennan suspects he was killed by the Ghost Killer but not enough evidence is left for an investigation even though everyone except Cam believes Brennan.
Bones: What do you think?
Booth: You know what? I think we're going to catch her.
The Jeffersonian team investigates the death of Stephanie McNamara, the daughter of a wealthy family whose remains were found in a national park. When the team digs deeper into the circumstances surrounding her death, clues from the case lead them to believe she may be the Ghost Killer's latest victim, with a surprising connection to a previous victim. It is later revealed that Stephanie is the Ghost Killer and is taking the fingernails as trophies to replace the ones she lost as a child. Her father had punished her by locking her into a stall in the family stable. Desperate to get out, she clawed at the walls, breaking off her fingernails in the process. Her killer is revealed to be a man her father framed for the murder of her first victim named Herman Kessler and later takes revenge on the judge that imprisoned him.
Bones: Stephanie glued those nails on herself. Stephanie McNamara was the Ghost Killer!
McNamara mostly targeted random victims and killed them through various ways, either making the deaths look like accidents and leaving the victims to be found or murdering them and then expertly hiding the bodies. Afterwards, she would remove the victim's right hand middle fingernail as a trophy and glue it to one of her own fingers to replace the nails she lost when she was younger. The exceptions to this selection method is her first two and last victims, who had a connection to her family.
- Giles McNamara (her father; helped pay off local officials to cover up her crimes)
- Leslie Dollinger (medical examiner; faked the ME reports in the Maya and Lana cases)
- Steven Paltor (judge; helped falsely convict Herman for Maya's murder)
- Glen Durant (blackmailer: used his connections at the FBI to destroy evidence)
- April 1994, unspecified location in Virginia: Maya Zinkow (raped by Giles McNamara and stabbed 16 times by Stephanie out of jealousy)
- Unspecified date and location in 1996, Maryland: Lana Brewster (stabbed)
- Unspecified date and location in 1999, Virginia: Carla Hopkins (bludgeoned)
- Unspecified date in 2002, Virginia: Michael Windsor (hanged)
- November 2004, unspecified location in Los Angeles, California: Heather Mendez (fatal car wreck)
- Unspecified date and location in 2008, Maryland: Chloe Campbell (stabbed)
- Unspecified date and location in 2010, Virginia: Alex Webber (shot)
- May 2012, unspecified location in Texas: Timothy Monroe (drowned)
- January 2014, Washington D.C.: Trent McNamara (shot in the temple, made to look like a suicide; framed for the murder of Lana Brewster)