As a teenager, Malachi had an incestuous relationship with his sister Magdalene, with the two having sex at a cabin in the middle of the local forest. Their acts were observed by an unidentified woman, known only as the "Appalachian Woman", who was apparently a hermit. Eventually, they accidentally conceived a son together; confused and panicking over their parents' reaction, the two decided to keep the baby in secret. When Magdalene finally went into labor in the cabin, Malachi fled in terror, leaving her to give birth to the baby alone with the help of the Woman, to whom she gave the baby away to. Out of shame for what happened, Magdalene later left the Lee family, and Malachi moved on, starting a new family of his own. Coincidentally, Magdalene eventually renamed herself Cissy and inducted herself into the Howard family, who had a longstanding, simmering feud with the Lees. Malachi later became the head of a business that only employed members of the Lee family (which he also apparently became the current patriarch of), which specialized in creating new and highly efficient conversion methods resulting in bio-fuels, which they intended to sell to a West Virginia energy company; the Howards also ran a similar business, which refueled the family feud.
On March 30, 2014, Matthias Lee, one of Malachi's sons from another woman, is killed by a bear-trap. When that is followed by the murder of Clark Howard, Cissy's son from her husband with the Howards (who also butted heads with Matthias several times), on the next day, Malachi is brought in for questioning and is interrogated by JJ. However, he is uncooperative, telling her that it is a family matter, and even insults her, derisively calling her wedding ring some sort of a symbol for the lesbian community. JJ then takes Malachi to an elevator, where they encounter Hotch and Cissy. Briefly surprised to see his sister Magdalene after so long, Malachi asks her if she visited her father's grave recently (a secretly message to her that he recognizes her), to which Cissy replies if he visited his (a secretly response to him). Later, his daughter-in-law Maddie is killed by being gruesomely decapitated by a moving car that dragged her. The day after her murder, the BAU find out about the Lee family business and drive over to a barn where their ingredients were being shipped over to, intending to investigate it. Mistaking the team for the Howards, Malachi opens fire on them with an assault rifle, but then, he immediately surrenders alongside the relatives who are with him after he realizes his mistake. He is then arrested.
When the BAU realize that Cissy is actually Malachi's sister Magdalene after she is abducted, they question him about why Cissy had been kicked out of the family, and he answers that she shamed her parents because she was pregnant. Hotch then deduces that it was his child after observing his behavior, to which he tells him that the sex was consensual and the two loved each other. He then tells the agent about his and Magdalene's discovery of her pregnancy and the plan they formed to keep the child and then get rid of it. Breaking down into tears, Malachi then adds about the time he fled when Magdalene went into labor. By the end of the episode, he is released from custody and encounters a shaken Cissy in the elevator. Wracked with guilt over what happened, he tells her that it should've been him who was killed, to which she replies, "It should've been us both." The two then go outside of the police station, where they are confronted by the entire Lee and Howard families.