John was last seen on November 16, 1996 with his mother, Sandra. The two had made plans to eat dinner at Sandra's mother's home in the vicinity of the 1100 block of University Drive in Bismarck, North Dakota. While on her way back to her mother's, Sandra called the Bismarck Police Department on her cellular phone. She sounded very upset and said she believed satanic ritual abuse was taking place on a farm near Center, North Dakota. She said she called the Bismarck police rather than Center police or the Oliver County Sheriff's Office because she did not trust them.

Sandra and John arrived at Sandra's mother's home at 7:30 p.m. Sandra appeared to be having mental health problems and she agreed to let her mother take her to the hospital. Before she went, however, she wanted to purchase gasoline. She and John were last seen leaving the residence in Sandra's gray 1990 Honda Civic. They did purchase fuel, but they never returned to Sandra's mother's home and have never been heard from again. Sandra's mother reported her daughter and grandson missing at 10:00 p.m. that same day.

Sandra's car was found abandoned the next day, at the Centennial Beach parking lot near to the Missouri River in Bismarck. There was no sign of John or Sandra at the scene. The driver's side door of the car was wide open, the keys were in the ignition, and Sandra's purse was sitting on the front seat, its contents undisturbed. Police searched the beach and the river and found a shoe that might have belonged to John. Strong river currents and severe weather hampered the search efforts and investigators could not search the river as thoroughly as they would have liked to. One theory is that Sandra murdered John and committed suicide by going into the river, but there is no hard evidence to support this.

Sandra separated from her second husband, John's father, three months before she disappeared. She was living in an apartment in Center, North Dakota with John and Spencer Nastrom, her sixteen-year-old son by a previous marriage. Sandra was very close to her oldest son, and her mother raised him after her disappearance. Nastrom's father was the victim of a homicide in 2005. He was run over by his own car and left to die in a ditch on a maintenance road north of Tuttle, North Dakota. His murder remains unsolved.

Police stated there is no evidence pointing to foul play in the Jacobsons' cases, and they have never had a suspect. Their cases remain unsolved. They were declared legally dead sometime after their disappearances.