Billy Milligan was born to Dorothy Sands and John Morrison on February 14, 1955, in Miami, Florida. Morrison, who worked as a comedian, struggled with depression and was heavily dependent on alcohol. He died by suicide when Billy was just 4 years old. After Morrison's death, Sands remarried her ex-husband, Dick Jonas, but the marriage ended soon after. In 1963, Sands married again, this time to a man named Chalmer Milligan (via The Dispatch).

Chalmer Milligan was an abusive stepfather to Billy. Based on medical reports from psychiatrists who treated him, the abuse from Chalmer was the root cause of his personality disorder. During talks with psychiatrists, Billy revealed that Chalmer sodomized and tortured him in various ways when he was just 9 years old. Chalmer denied all of Billy's allegations, and he was never apprehended. However, Billy's brother, sister, and mother attested to Chalmer's abusive nature during Billy's trial.

According to a timeline from The Columbus Dispatch, Billy started showing signs of instability after the abuse. His parents admitted him to a mental facility where he was diagnosed with hysterical neurosis. Months later, however, he was let go from the facility because of his troublesome behavior. He was also expelled from high school, and Billy then decided to enlist in the Navy at 17 years old.

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