Cooper was last seen walking to an arcade at Woodchuck RV Campground in Rancho, California, on December 13, 1986. She and her mother lived there. She has never been heard from again. Cooper was being supervised by a neighbor, William James Bannister, at the time she disappeared. Bannister was employed as a truck driver from Colorado in 1986. He had offered to babysit her when she and her mother went to work at an Old Town Temecula thrift store in Temecula, California that day. Bannister said he gave Cooper $5 to play video games at the arcade and she never returned home.

The day after Cooper's disappearance, Bannister went to his father's wedding reception in dirt-caked clothes. He told the other attendees that he had gotten dirty while participating in the search for Cooper. (In fact, he was not part of the search efforts.) He spoke to his father privately, then left the reception a short time afterward. That evening, Bannister's father told his new wife that Bannister had "done it again." Bannister had killed his girlfriend in San Diego, California in 1978, and served five years in prison for second-degree murder in that case. He was released from prison in 1984. After April's disappearance, in 1993, he tried to strangle his son's fourteen-year-old girlfriend in the back of his truck and was sentenced to sixteen years for attempted murder. When police searched the truck for evidence in that case, they found jewelry, bloodstained women's undergarments and several ligatures.

Bannister was charged with Cooper's presumed homicide in 1995, nine years after she disappeared. He was extradicted from Colorado to California for the trial. Investigators believed that he killed Cooper as part of a brutal sexual fantasy, then concealed her remains. His father was deceased by then, but Bannister's son testified that, in 1989, Bannister had told him Cooper was dead. Bannister allegedly stated Cooper fell off a rock and broke her neck while they were hiking together. He was convicted of her murder in 1998 and sentenced to life in prison without parole in early 1999. Authorities believe he may have also been involved in the disappearance of Laurie Lucas, a Colorado woman who vanished in 1990, but he has never faced charges in that case.

Cooper's body has never been located. She was a first-grade student at Cottonwood Elementary School in December 1986. Foul play is suspected in her disappearance due to the circumstances involved.