Brennan is spending her vacation down in New Orleans helping to identify human remains found in the aftermath of Hurricane Katrina. At the end of her penultimate day in Louisiana, a badly decomposed body, labeled John Doe 361, is brought into the lab with evidence of foul play. Brennan asks for x-rays to be taken of the remains. One of her coworkers, Dr. Graham Leger, asks her out to dinner that night and Brennan tells him she will see how the examination of John Doe's remains goes, and may take him up on his offer if she has time. The next thing she knows, Brennan wakes up lying on the floor of her hotel bathroom, covered in blood and badly beaten. She keeps getting quick flashes of a violent incident, but can't remember anything distinctly. Her hotel phone rings and it is the front desk letting her know that her airport shuttle is there to pick her up. Brennan tells the front desk there must be some mistake as she had scheduled the airport shuttle for Thursday. The receptionist informs her that it is Thursday, and Brennan realizes that she has lost an entire day's worth of memories.
Brennan goes to the hospital to be examined. There is no sign of sexual assault, but she did suffer a hairline fracture on her radius, a concussion, and a torn earlobe when one of her earrings was ripped out. Despite her injuries, Brennan can't help but feel regret over losing the earring, as it once belonged to her mother and is one of the few objects she has to remember her by. Brennan is visited in the hospital by Detective Harding, the same detective who brought Brennan the remains of John Doe 361 two days before. Detective Harding takes Brennan's bloody clothes in the hopes that they will contain blood from Brennan's attacker as well as Brennan herself. The last thing Brennan remembers is Dr. Leger knocking over a tray of instruments in the morgue, which happened just before John Doe's body was brought in. Booth also comes barging into the exam room, having flown down from DC after hearing about Brennan's attack. He is worried about Brennan's amnesia and asks for a tox screen to be run. Brennan's doctor informs him that a tox screen is in the works, but results will take at least 24 hours, as most of the area labs were destroyed by the hurricane.
Booth gives Brennan a ride back from the hospital. While they are in the car, Zack calls Brennan's cell phone to tell her that he reviewed the x-rays from John Doe 361 that Brennan sent him on Tuesday night. Brennan is confused, as she doesn't remember the case, or sending the x-rays. Zack informs her that John Doe's death was a murder, and he has what appears to be a bullet hole in his skull, although there is no apparent exit wound.
Brennan realizes she has no idea when she last ate, so she and Booth stop at a restaurant that Brennan and her fellow volunteers frequent. The waiter knows Brennan from her past meals there, and asks her how she sustained the injuries visible on her body. She tells him she's not sure what happened, but that it seems to have happened on Tuesday night. The waiter tells Brennan that she and an orderly named Sam Potter had dinner there at around 8:00 on Tuesday night, and Brennan was uninjured at that time.
Brennan and Booth go to the morgue to talk to Sam Potter. Sam, who practices voodoo, tells Brennan and Booth that Brennan invited him to dinner after finding a voodoo amulet, or gris-gris bag, in the mouth of John Doe 361. Sam informs them that this particular gris-gris bag is made from black gum root and is meant to silence the dead. He tells them that the charm is evil and must have been placed by a member of Secte Rouge, a subsect of voodoo that goes against the core principles of the religion and seeks to throw the forces of nature out of balance rather than maintain them. He tells them that there is only one shop left in New Orleans that sells black gum root, and it is run by a man named Richard Benoit. He also suggests that a spell could have been placed on Brennan, causing her to lose her memory, but Brennan insists she does not believe in such things.
Brennan and Booth visit the voodoo shop to speak to Benoit. Neither Benoit nor his daughter, Eva, recognizes Brennan. Eva pulls up a list of customers who have recently purchased black gum root at the shop, and Brennan is surprised to see the name of her colleague, Dr. Leger, on the list. She and Booth go to question Dr. Leger and find him brutally murdered and nailed to the wall of his bedroom.
Detective Harding comes to investigate the crime scene and interrogates Brennan about her involvement with Dr. Leger. Brennan tells Harding what they know so far about the gris-gris bag and the black gum root, but Harding makes it clear that she is finding Brennan's story harder and harder to swallow. Booth spots Brennan's missing earring on the floor in Dr. Leger's hallway and pockets it while everyone else's back is turned. Harding warns Brennan that if she finds any evidence tying Brennan to the crime scene, she will arrest her for Leger's murder.
Convinced there is a connection between Leger's murder and John Doe 361, Brennan and Booth return to the morgue to exam the latter's file. However, they find that the file and the remains themselves are missing and the only remaining evidence is the x-rays sent to the Jeffersonian before Brennan's attack. Unfortunately, Brennan's Jeffersonian colleagues aren't having much luck gleaning helpful information from the x-rays. There is evidence of trauma to the bones, but they cannot hypothesize a weapon without having access to the actual remains.
Brennan and Booth return to Brennan's hotel room, where Brennan frets over the fact that, objectively speaking, she could have killed Dr. Leger, as not only does she not have an alibi, but she herself doesn't know where she was or what she was doing at the time of the murder. Booth reassures her that, amnesia or not, there's no way she's capable of brutally murdering a colleague. Booth then discovers another gris-gris bag on Brennan's pillow, just moments before Detective Harding arrives to arrest Brennan for Leger's murder. Harding has found traces of Brennan's blood at Leger's home and Leger's blood on Brennan's clothing from the night of the attack. Booth tries to put up a fight, but Brennan insists on going quietly, not wanting Booth to do something he will later get in trouble for.
Booth asks his friend, federal prosecutor Caroline Julian, to fly to New Orleans to defend Brennan. When Booth and Caroline arrive at the police station, they find that Brennan is fully cooperating with the New Orleans police, telling them everything she knows. Caroline urges Brennan to clam up, making it clear that the police's case against her is a good one, and they will want to close the case quickly and easily.
Brennan is released on bail and she and Booth talk with Sam Potter again about the newest gris-gris bag Brennan found on her pillow. Booth describes the contents of the bag and Sam suspects it was designed to make Brennan forget. Brennan scoffs at the idea that a "forgetting spell" could be causing her amnesia, but Sam's version of events gains some credibility when Caroline arrives with the results of Brennan's tox screen, which came back completely negative.
Zack calls to tell Brennan that he was able to identify John Doe 361 based on evidence of a shunt that was visible on the x-rays. The victim's name is Rene Mouton and he was a well-respected voodoo priest who disappeared after helping several people to safety during the hurricane. Brennan and Booth search for Mouton's body in the coffins at the morgue, theorizing that the killer may simply have changed the nametag on Mouton's coffin to keep his remains from being discovered. Sure enough, they find Mouton's body in a mislabeled coffin, along with the fresher body of Mike Doyle, one of Brennan's colleagues at the makeshift morgue.
Another of Brennan's colleague's, Dr. Embry, performs the autopsy and determines that Mike was killed during or shortly after sex. Brennan remembers Mike telling her earlier about a fling he was having with a girl who liked to have sex in empty coffins. She tells Detective Harding that Mike's mystery girlfriend is the most likely culprit. Sam Potter asks for permission to sprinkle a sacred powder over the remains to purify them. After hearing the ingredients, Brennan assures Detective Harding that the powder will not contaminate the remains and she allows Sam to proceed. As soon as Sam begins to pour, the bones react to the electro-static charge of the mixture and show a pattern of bone bruising not visible to the naked eye. Booth recognizes the pattern as that of the grille of a classic Cadillac, and remembers seeing a picture of a Caddy with the same grille at Richard Benoit's voodoo shop.
Brennan and Booth arrive at Benoit's shop with Detective Harding, Sam, and Dr. Embry in tow. They believe that Benoit's daughter Eva is the killer, and that she murdered Mike when he wouldn't help her cover up Rene Mouton's murder. Benoit leads them to the basement, where he says Eva is praying, but they find Eva impaled on a spike protruding from the wall. Benoit tells them that Eva must have committed suicide to avoid being arrested for murder, but Brennan calculates that there is no way Eva could have gotten enough of a running start to propel the spike all the way through her spine, and must instead have been pushed onto the spike. Sam realizes that Benoit is the Secte Rouge sorcerer and that he murdered Eva believing he could bring her back to life, hoping that if all the evidence pointed to her, the police would stop looking for the killer. Brennan confirms this when she rips open Benoit's shirt and finds a wound on his chest from where the end of the spike stuck into him.
Back in D.C., Brennan and Booth fill the others in on their adventures in New Orleans. Hodgins is fascinated by the idea that a voodoo sorcerer put a forgetting hex on Brennan, but Brennan insists that her amnesia was drug-induced. Booth reminds her that her tox screen came back negative, but Brennan tries to account for this by theorizing that the delay in testing plus the adrenaline in her bloodstream forced the drug out of her system by the time the tox screen was run. She insists that objects have no intrinsic value and cannot be used to lay curses or spells. Booth then presents her with her mother's earring that he took from Graham Leger's house, an object which clearly has "intrinsic value" to Brennan, and Brennan realizes that he put his career on the line for her by stealing a piece of potentially incriminating evidence from a crime scene.