Daniel disappeared from the Lancaster, California apartment he shared with his mother, Denise Fagot, on March 2, 1989. They were last seen by Fagot's boyfriend, when he left their apartment go to work. Two hours later, Fagot's sister discovered them missing when she went to the residence to pick up her key. Authorities went to the apartment to investigate and found the front door open. The sliding glass door inside the residence was open a few inches as well, though it was a cold day. Police believe the door may have been forced open. A single muddy footprint was found on top of the air conditioning unit next to the sliding door, and the closet door in Daniel's bedroom was off its track.

Police initially believed that Fagot had left voluntarily with her son, but they now suspect foul play was involved in the disappearances. None of Fagot or Daniel's clothing or personal items appeared to be missing. Daniel's car seat and diaper bag had been left behind, and Fagot's vehicle was found parked undisturbed in its assigned space. Fagot had paid all of their utility bills for the month of March 1989 and they did not plan to travel. It is not known who apparently broke into their residence; Fagot and Daniel have never been seen again.

Fagot moved to Lancaster not long before her disappearance; she had broken up with Daniel's father and wanted to be closer to her family. Daniel's father lived in Orange County, California at the time of the disappearances. He was interviewed by police about their cases. Ten years later, he took a lie detector test about Daniel and Fagot's cases and failed. He has never been arrested in connection with his son and Fagot's disappearances, due to a lack of evidence.

Some agencies may classify Daniel's case as a family abduction.