"If anybody ever found us, remember what I told you. Daddy's the only one that loves you."
Thompson's mother died in childbirth, and his father Nate remarried a total of five times. Nate was a misogynist who abused and cheated on his wives, and these tendencies were passed on to his son. Nate was ultimately arrested for assaulting a prostitute. As an adult, Thompson became a repairman, founded his own business, and serviced several people. In his personal life, he developed severe obsessive-compulsive disorder and an obsession to start a family. One of his clients was an elderly woman named Clara Riggins, who was in frail health. Her condition led to her depending on him, and Thompson took advantage of her trustworthiness. When she died of natural causes, he buried her body in the backyard and took the house as his own, posing as Clara's grandson. In private, he converted Clara's basement into a torture chamber and began planning to abduct girls, being under the twisted belief that he would start a family. Thompson first started with Amelia Hawthorne, a girl in Indianapolis, in 2001. He renamed her Violet, physically and sexually abused her, and managed to brainwash her into believing she was his daughter. Through her, he fathered two girls, who he named Lily and Jasmine. Thompson then abducted two more girls, Gina Bryant and Sheila Woods, over the next eight years with Amelia's help, renamed them Rose and Daisy, respectively, and abused them as well. He tried to father a child through Sheila, but she suffered a miscarriage.
Thompson returns to the house one night while Gina is escaping. After Gina escapes, he goes down to the basement to check on the girls and realizes what happened. Amelia apologizes to him for not stopping Gina. He tells her that they need to go. Amelia tries to tell him Sheila is sick and needs help, but Thompson refuses, explaining that Sheila will slow them down. He then forcibly drags Amelia out of the basement, leaving Sheila behind. The next day, while Thompson is driving his van and Amelia is sitting in the back, she tells him she needs to use the restroom. Thompson replies that she will use it soon, but when Amelia keeps saying that she desperately needs to use the restroom because they have been driving for hours, he stops the van and abuses Amelia. Afterwards, Thompson apologizes for yelling, and Amelia accepts his apology. Later, he gives her a cheeseburger to eat. When she asks him if they can see Lily and Jasmine, Thompson tells her to be quiet and eat. After a while, he decides to rest for a moment and instructs Amelia to be quiet while he sleeps. As he rests, the BAU and local police show up, having identified Thompson as the unsub. Thompson is awakened by the BAU's presence. Morgan confronts him, tells him to put his hands in the air, and put his right hand on the door. When Amelia asks Thompson who they are, he doesn't respond to her question but reassures her that he is the only one who will love her. When Thompson opens the door, he starts running, but is tackled by Morgan soon after and breaks his wrist on a branch in the process.
Afterwards, Amelia is rescued and taken to the hospital along with Thompson. They are both separated in different rooms of the hospital. Thompson is interrogated by Hotch in his room; he tries to explain that he saved the girls because they were unloved by anyone, but Hotch doesn't buy it and tells him that Thompson raped and tortured them. Hotch then asks him about Clara; he explains that he didn't kill her, and claims that he found her lying on the kitchen floor and buried her body in the backyard. Later, Hotch confronts Thompson and tells him he knows that Sheila, who died in the hospital after being rescued, was pregnant and miscarried. Then, he tells Thompson that the team knows about Amelia's daughters Lily and Jasmine and asks him for their locations. Instead of answering Hotch's question, he says that he wants a deal, otherwise he won't say anything. Hotch reluctantly decides to go along with it and asks Thompson what he wants. He replies that he wants to do his time in a minimum security prison, and that he doesn't want to be sentenced to life as he doesn't want to die in prison. Hotch asks if that is all, and Thompson replies that he wants to see "Violet". When Hotch refuses, he tells him that he left Lily and Jasmine with enough water to last for only a few days and that he hasn't come back to see them in a week. He then says it will be Hotch's fault if they die.
Hotch doesn't have a choice and goes along with it, so he and Rossi take Thompson to Amelia's room. On his way there, he passes Sheila's mother Eileen, and Amelia's biological parents George and Maureen. When they step into Amelia's hospital room, Hotch and Rossi refuse to leave both Thompson and Amelia privately despite the former's requests, as it wasn't part of the deal. He then talks to Amelia and tries reassuring her of his love. However, during the conversation, Amelia has a flashback of Thompson raping and torturing her. George and Maureen step inside, which surprises Thompson. Amelia has another flashback of her past, remembers her real parents, and finally remembers her real name, much to the shock of Thompson and to the joy of her parents. Afterwards, Amelia begins to assault Thompson, prompting Hotch and Rossi to drag him out of the room. While Thompson is being dragged out, he yells "No deal". Afterwards, the BAU are able to find Lily and Jasmine in another house owned by Thompson and rescue them. Then, Hotch and Rossi are about to take Thompson to prison for his crimes, saying he will be sent to a federal prison for life because he withdrew his deal at the last minute. While they take Thompson out of the hospital, he is shot by Eileen in revenge for killing Sheila. She is then handcuffed and arrested by Hotch while bitterly watching Thompson taking his last breath. His body is then examined by a doctor.
Targeting eight-year-old Caucasian girls, Thompson lured them to his van in some sort of ruse (presumably by catching their attention with a puppy and then promising treats, like he did with Gina Bryant). Once they were at the van, he knocked them out, forced them inside, and drove them to Clara Riggins' house. There, Thompson held the girls captive in a basement in the homes for years, all the while physically and sexually abusing them, and also torturing them in a variety of ways. He would also make them wear gown-like outfits and give them names based on flowers. He was assisted by Amelia in his abductions of Gina and Sheila.
Thompson's crimes were most likely influenced by the mindset and actions of his father during his childhood. Children will do what they witness, and it is not uncommon for children to act or behave in the same way as their parents, which explains Thompson's extreme misogynistic tendencies and his violent streak. Thompson is intelligent and manipulative, as he not only took advantage to the woman whose home he used to hold his victims captive, but somehow managed to hold three girls hostage there for over a decade, which takes dedication and effort. His crimes were important to him, like a compulsion, and he gets off on having absolute power and control.
Thompson is loosely based on serial rapist and abductor Ariel Castro and was even compared to him by Rossi. Both abducted three females (one of whom was even named Gina) and held them captive in the basement of a home for the span of around a decade, during which time he physically and sexually abused them. One of their victims suffered at least one miscarriage, while another of their victims gave birth to at least one baby who was also held captive. Their crimes were eventually uncovered when one of the victims managed to escape, which led to the rescue of at least one other victim.
Thompson also has some similarities to Phillip Garrido, who abducted Jaycee Dugard in 1991 and held her captive until her rescue in 2009. Like Garrido, Thompson abducted a girl, physically and sexually abused her, and held her captive for over a decade. Both also fathered two daughters with their victims, taught said victims to address their daughters as their sisters (and vice-versa), and gradually allowed their victims to leave their residences intermittently.
- 2001, Indianapolis, Indiana: Amelia Hawthorne (abducted, physically and sexually abused, and held captive; was rescued on February 10, 2016)
- 2001(?), St. Louis, Missouri: Lily and Jasmine Hawthorne (his daughters with Amelia; held captive; both were rescued on February 10, 2016)
- 2006, St. Louis, Missouri: Gina Bryant (abducted, physically and sexually abused, and held captive; she escaped on February 9, 2016)
- 2009, Nashville, Tennessee: Sheila Woods (abducted, physically and sexually abused, and held captive; was rescued on February 9, 2016, but later died in the hospital on the next day from a septic infection induced by her captivity)
- Thompson is based on a few other unsubs on the show:
- Season Two criminal Michael Earlson. Both were abductors and preferential offenders who held their victims captive for years, sexually abused them, and made them believe their abductors were their fathers.
- Season Five criminal Robert Reimann. Both were preferential serial rapists, killers, and sadists who targeted females; held them captive for long periods of time; and had children with their victims by impregnating them via rape.
- Season Seven criminal Bill Rogers. Both were rapists who targeted at least one young girl, used ruses on them, held them captive for years, raped them with the intention of impregnating them, and were shot and killed by the mother of one of their victims for indirectly causing their deaths.
- Season Seven criminal Malcolm Ford. Both were killers and rapists who targeted women; sexually abused and tortured their victims, held them captive for years, impregnated them via rape, and would allow their female victims to see their children on certain occasions at another location to keep them compliant.
- Season Ten criminal John David Bidwell. Both were preferential offenders who abducted three victims (children in Bidwell's case, though they were abducted one at a time) and held them captive for long periods of time, had blue-collar professions and fathers whose actions caused them to commit their crimes, were indirectly responsible for causing the deaths of one of their victims, and were compared to and inspired by Ariel Castro.
- In addition, their respective episodes were both written by Virgil Williams.
- Season Ten criminal Alex Zorgen. Both were killers and rapists who operated in multiple states, abducted women, raped one of their female victims, which resulted in them having children, while also torturing and brainwashing them.
- The episode script expanded on Thompson's background slightly; his father suffered a massive stroke that partially paralyzed him. As a result, Thompson had to take care of his father for six months before a second stroke killed him. His father's death was the trigger for Thompson's abductions. This detail was excised from the final product for unknown reasons.