Searching the family's South Philadelphia walk-up the next day, police found a latch on the boy's bedroom door - so it could be locked from the outside.
The room was bare save for a urine-soaked crib mattress on the floor. The family lived just across the street from the Delaplaine McDaniel Elementary schoolyard, but no neighbors could recall ever seeing the boy playing outdoors.
Most neighbors said they didn't even know a young boy lived in the apartment.
From Khalil's scars, investigators believe he likely suffered regular beatings with belts and cords. The average weight for his age is at least 45 pounds, according to U.S. Centers for Disease Control and Prevention statistics.
Police would not discuss the circumstances of Khalil's death.
City officials, meanwhile, were trying to sort out why Khalil and his 3-year-old sister, Maya were living with their mother after Family Court judges had terminated her right to the couple's five other children.
Until age 2, Khalil had lived with foster parents - relatives of his father - and was thriving, a cherub-faced boy who was learning to count and recite his ABCs, according to his family.
In 2008, despite the pleas of his foster parents, extended family, and court-appointed caseworkers, Family Court Judge Charles Cunningham returned Khalil to his parents.
Mayor Nutter addressed the death at an unrelated City Hall news conference Thursday, saying that neither Khalil nor his sister had current cases involving the Department of Human Services.
"It's a very complicated matter," Nutter said. "There will be a full investigation. At a certain point in time, you'll know everything there is to know."
Citing confidentiality laws, DHS could not discuss the case, agency spokeswoman Alicia Taylor said. Family Court records are not public.
Cuffie and Hadi, whose birth name is Floyd Wimes, had seven children together, according to family.
At separate times, Family Court removed the five older children from the couple's care, according to sources close to the investigation. Both parents had drug addictions and neglected the older children, according to the sources.
Cuffie was convicted of welfare fraud in 1997, and still owes $4,224 of the $5,947 she was ordered to pay in restitution, according to court documents.
When Khalil was born, Hadi's parents asked his cousin, Alicia Nixon, 35, whether she and her husband could care for the child. Cuffie had tested positive for drugs while pregnant, relatives said.
Three of the older siblings had already been placed with other relatives, Nixon said Thursday, and the two other children were in foster care.
Nixon took in Khalil when he was a week old and soon filed for permanent custody.
At a custody hearing, a judge denied Nixon's request and returned Khalil to his parents. The court official made the decision without hearing from Khalil's caseworkers or child advocates, Nixon said.
"Our attorney was practically pleading and begging him to wait until he got the file," Nixon said. "But all Mom and Dad had to do was say they had a place to live and weren't on drugs anymore."
Four days after getting Khalil back, Cuffie and Hadi took him to the hospital filthy and dehydrated and in need of his asthma medicine, Nixon said. Nurses called DHS and Khalil was placed back in Nixon's care.
Nixon and her husband then became the child's legal foster parents - a rigorous process she said, involving classes and repeated DHS visits to her home.
The child did well under their care, she said. "He was a bubbly sweetheart," Nixon said. "He was a good little boy, very smart, and he thrived after the tug-of-war ended between us and his parents."
The court first granted Cuffie and Hadi weekly supervised visits, then overnight visits, Nixon said.
Nixon said she began keeping a video journal to document the change in the toddler's behavior after visits with his parents - how he seemed distant and angry for days afterward.
When Khalil was 2, Cuffie and Hadi filed for reunification, according to Nixon and sources closes to the investigation.
At a Family Court hearing in 2008, Cuffie and Hadi said they were off drugs and showed proof of housing, Nixon said. Hadi had work.
A court-appointed child advocate and a DHS social worker argued on Nixon's behalf.
"Our argument was they had five other children they lost, so why should they be entitled to this child and ruin his life?" Nixon said.
The boy was sent back to his parents.
Nixon and other relatives wrote letters of appeal to the mayor, DHS, and the judge, begging for the decision to be overturned. "We pleaded with everyone we could think of who might take pity on us," Nixon said.
A DHS social worker wrote back to her, expressing opposition to returning Khalil to his parents and apologizing that the department could not counter the judge's ruling, according to Nixon.
DHS monitored the child's care for a four-month transition period, according the sources. Then, keeping with policy, the agency closed the case.
DHS had not received any complaints about the child's care since 2008, the sources said.
On Thursday, Nixon and other relatives gathered to plan Khalil's funeral, their grief mixed with burning anger over the death of a child they feel was failed by the system.
"They gave him back to the very people who hurt him, and now we're getting him back dead," Nixon said. "We're sick and broken and there's nothing anyone could do or say that could give us comfort right now, except the fact that Khalil is no longer suffering at the hands of those monsters."
Contact Mike Newall at 215-854-2759, firstname.lastname@example.org, or follow @MikeNewall on Twitter.