"Baby Joe" had slipped out of the house before, his parents told reporters, but never in the middle of the night and never for this long.
Joe Clyde Daniels' parents told investigators that they went to wake the 5-year-old for school around 5:20am on Wednesday, but he was gone.
His parents said they usually located him within shouting distance of their house in Dickson, about 50 miles west of Nashville, Tennessee.
On Wednesday morning, the couple searched their property on Garner's Creek Road for an hour, then called police. The call led to a search that consumed their community and drew in hundreds of volunteers, all looking for an autistic 5-year-old who never talked.
Joseph Ray Daniels, 28, told Nashville ABC affiliate WKRN that he was afraid his son was "lonely, tired, scared and confused." They were hoping for the best, Daniels added, but they were still "really scared."
On Saturday, the search for a missing boy turned into a murder investigation after his father's confession, authorities said.
Daniels told investigators that he killed his 5-year-old son, according to the Tennessee Bureau of Investigation, then hid the boy's 65-pound body.
Daniels has been arrested and charged with criminal homicide, authorities said. He is being held in jail, with bail set at $1 million. It was unclear whether he had hired or been appointed an attorney.
"It's just been a devastating end to this, with our hope the whole time being that there would be a safe rescue," Sheriff Jeff Bledsoe told reporters.
" . . . A lot of people have poured their heart and soul into this in the community, and even outside of our community has rallied around each agency and organization there to support us and carry us through this week."
As authorities turned the rescue mission into a recovery mission and apprised the community of the criminal allegations, one question remained: Why?
Investigators have not released a motive - or even said whether Clyde gave one when he confessed.
Authorities did not immediately suspect foul play when Joe's family called them Wednesday.
"My son has disappeared and we cannot find him," his father told the dispatcher who answered his call, according to a 911 recording obtained by Nashville ABC-affiliate WKRN.
"He is 5 and has autism. . . . He must have unlocked the door. He got out."
A person passing by the family's house around 1 a.m. reported seeing what appeared to be a boy within 100 yards of the family's home.
Over the ensuing three days, hundreds of neighbours who heard of the disappearance volunteered to join the search, coordinating their efforts at a nearby Baptist church where a mobile command center had been set up.
The search was expanded to a one-mile radius, then a three-mile radius. Investigators examined what appeared to be a child's footprints, drained a pond and followed search dogs who indicated that they'd picked up the child's scent. All were dead ends.
On Friday, Daniels told WKRN that the family was still worried about their child.
A day later, the Tennessee Bureau of investigation said it had an update.
"This is not the news that anyone wanted to hear," the bureau said in a statement posted on its Facebook page around noon Saturday.
"The father of the Dickson County child who was the subject of an Endangered Child Alert this week has been arrested and changed with the homicide of 5-year-old Joe Clyde Daniels."