The discovery marked a bizarre end to a saga that started when the giant silvery balloon floated away from the family's yard Thursday morning, sparking a frantic rescue operation that involved military helicopters and briefly halted some departures from Denver International Airport.
Then, more than two hours after the balloon gently touched down in a field with no sign of the boy, Sheriff Jim Alderden turned to reporters during a news conference, gave a thumbs up and said 6-year-old Falcon Heene was at his house.
"Apparently he's been there the whole time," he said.
The confusion over whether the boy was in the balloon arose as the family tinkered with the craft Thursday and Falcon's father scolded him for getting inside a compartment. He said Falcon's brother saw him inside the compartment and that's why they mistakenly thought he was aboard the balloon when it launched.
Photos: The "Balloon Boy" Incident
But the boy had fled to the garage, climbing a pole into the rafters and hiding in a cardboard box, at some point after the scolding and was never in the balloon during its two-hour, 50-mile journey through two counties. "I yelled at him. I'm really sorry I yelled at him," Richard Heene said, choking up and hugging Falcon to him during a news conference.
"I was in the attic and he scared me because he yelled at me," Falcon said. "That's why I went in the attic."
Heene said the balloon wasn't tethered properly, and "it was a mishap."
"I'm not going to lay blame on anybody," he said.
The boys' parents - Richard Heene and his wife, Mayumi - are storm chasers who appeared twice in the ABC reality show "Wife Swap," most recently in March. The show promoted the Heene family as storm chasers who also "devote their time to scientific experiments that include looking for extraterrestrials and building a research-gathering flying saucer to send into the eye of the storm."
CBS News Correspondent Ben Tracy reports the Heene boys have several videos on YouTube.
The Family behind the "Balloon Boy" Story
Richard Heene said the family had been working on a low-altitude vehicle that people could take out of their garages and use to hover over traffic. But it wasn't supposed to go higher than 20 feet or so, he said.
Richard Heene adamantly denied the notion that the whole thing was a big publicity stunt. "That's horrible after the crap we just went through. No."
During a live interview with CNN, Falcon said he had heard his family calling his name.
"You did?" Mayumi Heene said.
"Why didn't you come out?" Richard Heene said.
Falcon answered, "You had said that we did this for a show."
Later, Richard Heene bristled when the family was asked to clarify and said he didn't know what his son meant. He didn't ask his son what he meant by "a show."
"I'm kind of appalled after all the feelings that I went through up and down that you guys are trying to suggest something else," Richard Heene said.
Richard Heene told KUSA-TV in Denver that he thought his son was referring to earlier in the day when he showed reporters his hiding spot. He didn't return a message from The Associated Press.
The sheriff was already planning to meet with investigators Friday to see if the case warranted further investigation. After the CNN interview, Alderden told the AP: "It has raised some questions. Our personnel who were dealing with the family all day are convinced this is a legitimate incident and this is not a hoax."
Still, in light of the interview, Alderden said, "We intend to go back and further ask the family to cooperate with our investigation through answering more questions and resolve this issue."
Earlier Thursday, the sheriff said he would meet with investigators on Friday to see if the case warranted further investigation.
The flying saucer-like craft tipped precariously at times before gliding to the ground in a dirt field 12 miles northeast of Denver International Airport. Sheriff's deputies secured it to keep it in place, tossing shovelfuls of dirt on one edge and poking holes to let the helium out.
With the child nowhere in sight, investigators searched the balloon's path. Several people reported seeing something fall from the craft while it was in the air, and yellow crime-scene tape was placed around the home.
Neighbor Bob Licko, 65, said he was leaving home when he heard commotion in the backyard of the family. He said he saw two boys on the roof with a camera, commenting about their brother.
"One of the boys yelled to me that his brother was way up in the air," Licko said.
Licko said the boy's mother seemed distraught and that the boy's father was running around the house.
Licko said he didn't believe any hoax was involved.
"Based on what I witnessed in the backyard in the morning with the parents, I don't think that's the case," Licko said. "They're better actors than I thought they were if that's the case."
In a 2007 interview with The Denver Post, Richard Heene described becoming a storm chaser after a tornado ripped off a roof where he was working as a contractor and said he once flew a plane around Hurricane Wilma's perimeter in 2005.
Pursuing bad weather was a family activity with the children coming along as the father sought evidence to prove his theory that rotating storms create their own magnetic fields.
Although Richard said he has no specialized training, they had a computer tracking system in their car and a special motorcycle.
While the balloon was airborne, Colorado Army National Guard sent an OH-58 Kiowa helicopter and a Black Hawk UH-60 to try to rescue the boy, possibly by lowering someone to the balloon. They also were working with pilots of ultralight aircraft on the possibility of putting weights on the homemade craft to weigh it down.
Alderden said he didn't have an estimate of how much the search cost. Capt. Troy Brown said the Black Hawk helicopter was in the air for nearly three hours, and the Kiowa helicopter was airborne for about one hour. The Black Hawk costs about $4,600 an hour to fly, and the Kiowa is $700 an hour, Brown said.
Col. Chris Petty, one of the pilots aboard the Black Hawk, said he was thrilled the boy was OK.
Asked what he would say to the 6-year-old if he saw him, Petty said: "I'm really glad you're alive, I'm very thankful, but I'd sure like to know the rest of the story."
The episode led to a brief shutdown of northbound departures from one of the nation's busiest airports between 1 p.m. and 1:15 p.m. MDT, said Lyle Burrington, the National Air Traffic Controllers Association representative at the Federal Aviation Administration's radar center in Longmont, Colo. The balloon was about 15 miles northwest of the airport at that time.
Before the departure shutdown, controllers had been routing planes away from the balloon, Burrington said.
Jason Humbert said he was in a field checking on an oil well when he found himself surrounded by police who had been chasing the balloon.
"It looked like an alien spaceship you see in those old, old movies. You know, those black-and-white ones. It came down softly," Humbert said. "I asked a police officer if the boy was OK and he said there was no one in it."
Mayumi Heene told CNN she was speechless when she saw her son.
"He scared the daylights out of us," Richard Heene told CNN. "I just asked him to please never do that again."