On May 8, almost five months after the incident with Ms. Warner, nine year old Becky O'Connell disappeared while walking to the S&A Convenience Store on North Drive and Main Avenue to buy some candy. The next day, two men driving ATVs found her battered body along the Big Sioux River near Lake Alvin in Lincoln County. Becky had been vaginally and anally raped and stabbed multiple times. The ultimate cause of death was a throat wound that punctured her jugular vein. Witnesses had reported seeing a light blue Chevrolet truck near the area where Becky's body was found, and they gave a description of the driver to police.

Since Moeller owned just such a truck, he was quickly taken in for questioning by Sioux Falls police. He offered blood and hair samples, but denied having anything to do with Becky's death. However, the next day he skipped town, leaving his truck behind. Police obtained search warrants for the truck and his trailer. Mud collected from under the truck was found to be similar to the natural area near where Becky's body was found and had some unusual soil not commonly encountered in many locations. Semen found on the victim would be DNA matched to Moeller. He was charged with the rape and murder of Becky O'Connell but it would be eight months before he was spotted in Tacoma, Washington, some 1,200 miles away, arrested, and extradicted to South Dakota to stand trial.

Lincoln County Sheriff Ken Albers had the unfortunate task of participating in the collection and processing of Becky's body. He said "It was laying out there and it just looked like a doll. I wondered if I wasn't being made a fool of, if someone hadn't been playing a prank on us. I had to reach out and touch the body before I knew it was real." It had rained the day of the murder and it was speculated that Moeller had offered Becky a ride in his truck to give her some shelter from the rain.