The Apprentice is the former apprentice of The Gormogon and the real killer of the lobbyist Ray Porter during Season 3. He was declared dead by Zack Addy in The Perfect Pieces in the Purple Pond and his body found by Doctor Jack Hodgins with help from Doctor Gordon Wyatt and Angela Montenegro in The Steal in the Wheels in Season 12.
At the end of episode, when Ray Porter returned to his home, he is assaulted by an unknown assailant who was hiding in his closet with a dagger in his hand and was murdered after being stabbed in the heart. The same night of Porter's killing, Gormogon killed his former apprentice to make a place for Zack.
Zack confessed to the murder of Ray Porter and was sent to McKinley Psychiatric Hospital instead of a prison.
When he returned to the asylum after helping the team solve the murder of Jared Addison, Zack tells Sweets that, while he had helped Gormogon find the lobbyist, he himself had not actually stabbed him. In other words, Zack believes he killed the lobbyist; but, from a legal standpoint, he is considered only an accessory or co-conspirator. Sweets insists Zack change his story, but Zack refuses. He fears, if his secret were to come out, Booth will take him out of the sanitarium and throw him in prison, where he is assured by Hodgins to do very poorly. Sweets wanted him to change his story because he believes that the real killer is still out there, but Zack told Sweets that Gormogon killed him in order to recruit Zack since "there could only ever be two." He reminds Sweets, as Zack's therapist, he must not reveal his secret because, if Sweets were to do so without his permission, he would be violating doctor-patient confidentiality. The episode ends with Zack at the institution and Sweets keeping Zack's secret, despite his visible worries about Zack.
Zack confessed to Booth and Brennan that he never killed Ray Porter. He confessed because he assumed that he would kill if The Master asked him to, but after having a chance to kill The Puppeteer and ultimately refusing to finish the job, he learned that he is not capable of killing, not even to save himself. He decides that the time has finally 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.
Trying to exonerate Zack, Hodgins finds microbial evidence that Brennan missed pointing towards the true killer of Ray Porter. However, Cam refuses to accept it and accuses Hodgins of tampering with evidence to get Zack freed. Despite telling Hodgins she won't accept the evidence, Cam goes over it after he furiously leaves.
In an attempt to overturn Zack's sentence, Booth summons Dr. Gordon Wyatt to observe Sweets's notes on his meetings with Zack when the Gormogon case hits a dead end. While Wyatt can't find anything, he instead suggested to Hodgins that they locate the body of the Apprentice instead and search it for evidence in Ray Porter's murder. Wyatt deduced that in the eyes of Gormogon, The Apprentice failed him as he wasn't as good as Zack, so he wouldn't treat the body with reverence. Gormogon wouldn't have cannibalized on his remains because they were probably poisonous to him, symbolically. He also wouldn't be deposited into some shallow grave since Gormogon was a slave to carrying out ritualistic rites during his crime spree like the Freemasons. The bones wouldn't have been added to the Silver Skeleton of the Widow's Son because he was a traitor. Hodgins also stated that the remains of the Apprentice had to be somewhere in the D.C. area since Zack told them that Gormogon was only gone for a few hours when he went to dispose of the corpse.
Hodgins and Wyatt searched through the historical information in the Gormogon Vault for clues with no luck at first. After Wyatt theorized that he was buried under a Masonic ritual symbolizing betrayal, Hodgins theorizes that the Apprentice was likely buried under an Acacia Tree. While the Acacia Tree symbolizes the immortality of the soul, it is also inedible and poisonous as the Apprentice would've been to the Gormogon, thus making it the perfect place to bury a poisonous outcast apprentice. The two then enlisted the help of Angela Montenegro who displayed a map of Washington, DC with the original boundary lines before Virginia reclaimed everything west of the Potomac in 1792. Knowing that the Apprentice must be in the DC area as Zack stated that the Gormogon was only gone for a few hours after killing the Apprentice, Hodgins has Angela get him the locations of all of the Acacia Trees on the west side of the boundary as, to the Freemasons, the west and the setting sun symbolized finished projects and death.
After getting the location of the Acacia Trees, Hodgins led a team to search them for the Apprentice's body. After searching at least four Acacia Trees with no luck, Hodgins and his team eventually found and exhumed the Apprentice who had been buried in an inverse Masonic coffin. Accompanied by Camille Saroyan, Hodgins opened the coffin to find the Apprentice's skeleton with his clothes perfectly preserved. On the Apprentice's right cuff, Cam noted dried blood, presumably Ray Porter's and thus the evidence needed to prove the Apprentice killed him and exonerate Zack was brought into the light.
Zack faces a judge in his appeal where Hodgins testifies to the fact that the blood found on the Apprentice's cuff was an exact match for Ray Porter, proving that the Apprentice killed Porter, not Zack. Caroline Julian argues that Hodgins could've planted the evidence due to its unusually compelling nature after so many years have passed since the case was presented, but Hodgins testifies that while examining the Apprentice's body, he established a protocol so that no one would examine the remains or any case-related evidence alone in the lab to prevent someone from doing such a thing and to ensure that no such allegations could be brought against anyone in court.
Based on the new evidence, the judge overturns Zack's murder conviction and life sentence in the murder of Ray Porter. However, while the evidence exonerates Zack of murder, it does not clear him of the charge of aiding a known killer and he will have to finish out the last thirteen months of his sentence on that charge. While Brennan is disappointed that Zack could not be immediately released, he accepts the verdict with grace as thirteen months is nothing compared to the life sentence he faced before. Caroline Julian is revealed to have been helping Zack as well subtly by reminding the judge multiple times of the compelling new evidence found with the Apprentice's body.
- Ray Porter (Died on November 27, 2007)
- The Perfect Pieces in the Purple Pond (mentioned only)