His Modus Operandi involves the victim being taxidermied, dressed in old fashioned clothes and trinkets, treated like people who are still alive, and hoisted as a marionette. In the Season 11 finale, the Puppeteer's identity is falsely revealed to be Zack Addy, the former professional forensic anthropologist who worked for the Jeffersonian who was sent to McKinley Psychiatric Hospital for his role in the rampage of another previous serial killer; The Gormogon. In the Season 12 premiere, at the end it was revealed to be Zack's doctor, Mihir Roshan, who framed Zack and made him believe he was actually the killer.
The dead body of a social worker found in a park reveals clues suggesting that the killer lived with the body for months before dumping it. The body had chipping on the teeth which suggest that they were fed porridge with a spoon by the killer after they were dead. The discovery of a set of remains in Limbo with similar anomalies on the bones as the current victim which was killed six months prior to the current victim's time of death confirms it's a serial killer who poisons their victims with a lethal dose of Propofol and Succinylcholine and uses the corpses as marionettes. Brennan hints that she and the killer are similar in many ways. Brennan blamed herself and Booth for the serial killer's rampage. She remarks that given their track record with catching killers, it would be statistically more likely that if they never quit their jobs, then Allison Monroe would still be alive. At the end of the episode, The Puppeteer is seen elsewhere in a room full of wooden dolls and mannequins hanging like puppets. The killer is on a laptop observing Brennan and Booth through the recorded video from a surveillance camera that was found in the kitchen of the house of one of the suspects. The case still remains unresolved and the serial killer is still at large.
Brennan, Hodgins, and Angela are seen in the Jeffersonian looking at a burning victim. Hodgins notices that the victim is bleeding, but Brennan stated that the dead don't bleed after death. Angela stated to her that "old wounds can cut deep." Brennan looks more closely at the victim, but he suddenly wakes up, alive and in agony. Brennan suddenly wakes up in Booth's car from that nightmare and into reality. They were on their way to a crime scene when Brennan fell asleep for 30 minutes. Brennan stated that she hasn't been sleeping since The Puppeteer missed his interval a few days prior to the current date. Booth tries to reassure Brennan that there was nothing that either of them could have done to stop The Puppeteer, however Brennan tells him that his words are having the opposite intended effect and tells Booth that she will sleep when this serial killer is caught.
The dead body of a woman was found dressed like Brennan, leading everyone to believe that she is The Puppeteer's real target. The victim, Melissa Goodman, was found in an old classroom wearing a more contemporary outfit than the previous victim. Brennan claimed that she used to own one that looked just like it before she had recently donated it to the Women's Mission Center (Possibly during the events in The Head in the Abutment.). Booth found a sales tag from the Women's Mission Center, which has proven that the clothes the victim is wearing are Brennan's clothes. They find that the woman was groomed to look like Brennan in many more ways than one and the killer even spoon fed the victim one of Brennan's favorite meals; seitan with piccata sauce. Hodgins was seen to have been improving on the gradual regeneration of his legs when he mentioned that the killer wiped the shoes of the victim clean before applying mud to them to mislead the team and delay the progress of the investigation. The serial killer is then seen listening to a childhood song; Frère Jacques, while simultaneously working on a puppet. In the background, it is shown that he has a board of dolls with pictures of the whole bones cast to replace the faces.
Booth and Brennan then move to interview the latest victim's therapist. Brandon Faulk says that the victim had a nightmare that she was going to die. Brennan inevitably falls asleep from all the nightmares she's been having herself. She is then shown in her office, looking at the files of previous cases involving victims that have been incinerated when Wendell comes in and hands her a cup of coffee and leaves to go back to the bone room. Once he left, the lights shut down and Brennan was left alone. She tries to protect herself with a bottle of hydrochloric acid until she finds the burning victim from her previous nightmare, still alive, walking towards her. She screams, awaking from that nightmare. She wakes up in her office again, with Wendell walking by and coming in to ask what's wrong. He then holds her hand assuring her everything will be alright until Brennan sees that Wendell's hand is burned significantly and he says "If you knew what I knew, you'd be so proud of me." She then awakens from that nightmare into reality. Brennan decides to see the therapist of the victim, despite the fact that she doesn't believe in psychology, which, as she stated, expresses her desperation to make the nightmares stop.
Booth and Aubrey have a lead on a puppeteer. They eventually find the Puppeteer's lair in the guy's basement and they even found that the puppet that the Puppeteer was working on earlier was made to look like Brennan. They bring Graham Reynolds into custody trying to ask him who rents his basement, but he claims to have never known his name or seen his face. He mentioned that he tried to see his face once because of his curiosity and he remarks that he "shouldn't have" tried to see his face. When he and Aubrey were looking over the evidence they have regarding the victims, suspects, and the Modus Operandi of the killer, Booth then realizes that the therapist could be the killer. Meanwhile, Brennan is seen in a hypnotic state and cooperating with the therapist by telling him what or who she saw in her dreams. Booth barges in and arrests the therapist, but Brennan believed Dr. Faulk to be innocent and barged out of the interrogation room after having a heated argument with Booth.
While Booth prepares to interrogate the therapist, Brennan returns to the lab while the rest of the team is out. They were sent a message from "Brennan" telling them to shut down the lab and meet them at the Founding Fathers, but Brennan never sent any such message. She then realizes who the killer is as the killer himself walks in, hangs up the phone call, and captures her. Booth discovered that The supposed Puppeteer abducted Brennan and persuaded Dr. Faulk to give him the notes he took when he was talking with her in his office. The rest of the team joins back together and puts together the clues which could identify who the killer might be. Aubrey found out that the killer was musical and likely born sometime after 1978 in Michigan through a song book, with all the songs left in the mix tapes in order which was published in 1978 in Lansing, Michigan, that his Aunt Donna gave him. Through the killer's analysis of the people he worked with and his obsessive analysis on Brennan, Angela deduced that in terms of mathematical and computational linguistics, that the killer is off the charts. Through the way that the bodies were taxidermied and the bones re-articulated and frequently re-positioned, Cam added that he knows Human Anatomy. Hodgins deduced that the killer knows about Robotics or Applied Engineering through the way the killer made a believable counterfeit message which looked like it came from Brennan. Based on the injuries on Melissa Goodman's skeleton, Wendell deduced that the killer is physically declined since he struggled to abduct his most recent victim. Booth, after reading Brandon Faulk's notes on Brennan's nightmares, found out that she mentioned Wendell during their meeting, but she mentioned that his hands were burned as if they were in some kind of an explosion. Aubrey stated that Wendell couldn't be the killer since his hands were never crippled by an explosion. Hodgins stated that Wendell could be a symbol of the person they are looking for. Booth suddenly realizes who the killer may be through the burned hands mentioned in her most recent nightmare and realized that The Puppeteer was someone who used to work at the lab. As Booth leaves, Cam realized what he was thinking and remarks that "it can't be." He then barges into McKinley Psychiatric Hospital and heads into one of the rooms. The Head Nurse runs after Booth to stop him, but stops after Booth turns over a bed cover which was covering a big pile of hard-cover books rather than the person he is looking for. The Head Nurse leaves to call security and Booth stares up at the sky and wonders where The Puppeteer took Brennan, if she was still alive. Brennan then wakes up to a familiar face and voice in an unknown location, the man with all the clues and all the smarts. The person who abducted Bones is revealed to be Dr. Zack Addy, Brennan's original assistant.
In the Season 12 opener, the show picks up right where Season 11 left off-road Brennan with Zack, Booth rushing to the rescue, and the squints helping. The location that Zack took Brennan to was the basement of the Jeffersonian inside The Gormogon Vault. Thanks to Hodgins, they find Brennan with Zack in the basement, with Brennan stopping Booth from shooting Zack who was pleading to both Brennan and Booth that he never killed anyone and even attempted to inject himself with a syringe of Sodium Thiopental; truth serum, to convince Brennan that he was telling the truth. Booth arrested Zack and refused to believe that he was innocent after finding Brennan, who believed that Zack might be innocent.
Throughout the episode, different people doubt at different times whether Zack was The Puppeteer or not. Mihir Roshan, Zack's Psychiatrist, brought his possessions to Booth and Brennan. He told them about how Sweets was visiting Zack almost every week and that Zack had trouble processing when Sweets died. In the process, he went into a fit of rage and caused a self-inflicted injury to his forehead. Aubrey discovered from Zack that he was hacking into the E-mail accounts of everyone at the Jeffersonian to catch up with how they are doing. Angela discovered that he adopted the alias; Dr. Alexander Bancroft; Hodgins' doctor to restore the feeling in his legs. Zack developed the procedure that was helping Hodgins recover from being paralyzed, but he told Hodgins that there is a less than one percent chance that it will work. He felt ashamed that he wanted to give Hodgins hope, but ended up giving him more pain. Brennan discovered a tooth fragment that did not belong with the other victims, so she and Wendell went back to The Puppeteer's Lair in Graham Reynolds' basement. Wendell discovered a hidden compartment behind a false wall which was hiding half of the remains of another teenage person who was exhumed between ten and twenty years ago. Karen Delfs returned from Kansas City and she discovered that The Puppeteer was suffering from D.I.D. (Dissociative Identity Disorder) and partially believed that Zack's head injury might have caused it. Brandon Faulk told Booth and Brennan that she never equated Zack with The Puppeteer, which indicated that she believed in his innocence and that whoever the Puppeteer is has a pathological need for control, to get as close to them as possible, and steer the investigation. Brennan and Karen wanted to allow Zack to go through the evidence files believing that the other identity will present itself. Zack remembered Karen from when she was working on her dissertation and granted her a series of interviews. He told them that he had blackouts, but he believed that it might have been caused by changes in his medications. After thoroughly examining the evidence, he told Dr. Roshan that he wants to go back to McKinley Psychiatric Hospital, this time to Maximum Security. Zack and Brennan have convinced themselves that the circumstantial evidence that Zack is The Puppeteer is conclusive.
After Booth drops Zack off at McKinley Psychiatric hospital, Brennan calls him telling Booth to go back for Zack because they discovered that Roshan is actually The Puppeteer. The team discovered that the fourth victim that they found in The Puppeteer's Lair was not a victim, but the exhumed conjoined twin brother of Mihir Roshan. Karen determined that the personality of Roshan's deceased twin was in conflict with Roshan himself after they were separated. The scene switches to the sanitarium where Zack was almost poisoned by Roshan and attacking the deranged doctor to defend himself, getting the chance to kill him in self-defense but ultimately could not do it. He stabbed Zack in the leg with his pen to disorient him. Before Roshan could kill Zack, Booth barges in and shoots him in the back of the spine, killing him and saving Zack.
To Zack, his inability to kill Mihir Roshan, even in self-defense, proves he never would have killed anyone, even if The Master had asked long ago, so now he has the strength and courage to fight his conviction. It also proved Sweets' theory from The Perfect Pieces in the Purple Pond that Zack, at heart, is not a killer and deserved to be released. As Booth and Brennan told Zack that they will have him transferred to another facility, Zack confessed to them that he never killed Ray Porter and that the time has come for him to re-enter society. Brennan agreed to re-examine the evidence on Ray Porter's remains to find the real killer and Booth agreed to help release Zack believing that he has served his time. As a result, Zack is ultimately exonerated of Ray Porter's murder in The Day in the Life.
- Douglas Burkhart (Died May 10, 2015)
- Allison Monroe (Died November 13, 2015)
- Melissa Goodman (Died May 17, 2016)
Victims by Proxy Edit
Known Associates Edit
- George Gibbons (Finds victims for The Puppeteer, Deceased.)
- Graham Reynolds (Provided shelter, unknowing.)
- According to Michael Peterson, the Puppeteer arc is a nod to an episode of The X-Files; Home. This explains why the mix tapes left by The Puppeteer were labeled "Home."
- The songs on the mix tapes left by the victims are childhood classics:
- The events in The Puppeteer Episodes are reminiscent to some of the events in the Nightmare on Elm Street movie franchise. The victims having nightmares before they are murdered, the killer having burn marks, scars, and wearing gloves (Minus the razors.), the real killer's body being deceased and the soul and identity of the killer to be very much alive inside of another living person as was shown in the second movie; Freddy's Revenge, even one of Kreuger's victims was controlled as a marionette before his death in the third movie; Dream Warriors implying their relations to The Puppeteer Episodes. Ironically, Booth mentioned Freddy Kreuger in The Monster in the Closet.