Morales was last seen in the New York City borough of Brooklyn sometime in November 1995. She lived on Halsey Street in Bedford-Stuyvesant at the time, and attended Public School 1. She was frequently absent and one of her relatives complained about her truancy to the Bureau of Child Welfare (BCW). The BCW opened a case for Morales. The caseworker couldn't find any evidence that she was abused. Morales's mother, Denise Solero, withdrew her PS 1 in November 1995 and said she was moving and would transfer Morales to PS 93, which was in another district. Morales was never re-enrolled in school anywhere, however. Solero told the neighbors she had sent Morales to go live with her father out of town, but this wasn't true either. The BCW closed her file in February 1996, not realizing no one had seen her in four months.

In February 1997, a friend of the family went to police and said Morales had been killed. Solero's boyfriend, Luis Santiago, was later charged in her death. Santiago had been physically and sexually abusing Morales for years. He also beat Solero, who was living in a shelter for battered women when Morales was reported missing. She pleaded guilty to hindering prosecution and agreed to testify against Morales. In return, she was sentenced to probation instead of a prison term. Santiago confessed to Morales's murder, saying he had unintentionally killed her when she got in the way while he was beating Solero. Solero disputed Santiago's version of events, however. She said he had become enraged when Morales refused to take a bath, and he beat and asphyxiated her while Solero held her down. Morales died on December 31, 1995.

Santiago was acquitted of murder charges, but convicted of second-degree manslaughter and evidence tampering at his December 1997 trial. The manslaughter conviction indicated the jury believed his version of events rather than Solero's. He was sentenced to six and a half to nineteen years in prison. Solero was given a five-year term of probation. She was forbidden to have any contact with her other two children, and was ordered to notify the Probation Department if she became pregnant again. Many criticized the deal as being too lenient, but prosecutors said Solero's testimony was crucial in the case against Santiago and they hadn't known how deeply involved she was in Morales's death until after they had agreed to give her probation.

Santiago and Solero said they wrapped Morales's body in a trash bag and dumped it in a vacant lot. Authorities believe her remains were hauled away with the rest of the garbage when the lot was cleared. Her body has never been found, but foul play is suspected in her case due to the circumstances involved.