Bowman was reportedly last seen at home on January 7, 2003, but his mother did not report him missing until January 23, over two weeks after his disappearance. She could not explain the reasons for the delay. A month after Bowman's disappearance, his mother, Cynthia Lee Davis, was charged with child endangerment. Bowman was scalded on his legs, feet, groin, and buttocks before his disappearance and Davis never took him to a doctor. Davis's boyfriend, Dennis Schermerhorn, was also charged in connection with the incident. Authorities stated Schermerhorn gave conflicting statements about Bowman's case.

Teachers at Bowman's school say they noticed bruises on his body in December. They did not report this until after he disappeared. Bowman's father last saw his son at Christmas in 2002. He had weekend visitation rights, but Davis and Schermerhorn would not permit him to see Bowman after Christmas, saying he was ill. Bowman's father is not considered a suspect in his son's disappearance. Davis and Schmermerhorn only reported Bowman missing after his father threatened to call the police himself. In April 2003, Davis and Schmermerhorn were indicted on two counts each of child neglect. The first count relates to their failure to seek medical attention for Bowman's burns; the second, for failure to report him missing for two weeks. In July of that year, they were charged additionally with felony murder.

Davis pleaded guilty to the charges and was sentenced to fifteen years in prison and twenty years of probation. She testified against Schmermerhorn. She claimed that Logan burned himself in the bathtub on or about January 7, and and she wanted to take him to a hospital, but Schmermerhorn told her to calm herself first. Davis fell asleep and when she woke up, Bowman was gone. Schmermerhorn told her he had taken the child to his mother, a nurse. Davis says she never saw her son again. Schmermerhorn says it was Davis who left with Bowman and later returned without him. He stated he believed Davis had sold the child.

In May 2004, a judge dismissed the murder charge and one of the child neglect charges against Schmermerhorn, citing lack of evidence. Prosecutors were counting on Davis's evidence to convict him, but her testimony was self-serving and inconsistent. She has told five different stories about the events of January 7. Schmermerhorn was convicted of one count of child neglect and sentenced to a year in jail.

Bowman has not been found. Foul play is suspected in his disappearance due to the circumstances involved.