Story highlights Autopsy shock: Teen's organs removed, cavity filled with newspaper 
 
 "We thought we were burying Kendrick, not half of Kendrick," father says 
 
 Kendrick Johnson was found dead in a rolled-up gym mat in January 
 
 His death was ruled accidental; a private autopsy challenged that finding 
 
 The death of 17-year-old Kendrick Johnson was awful enough for his parents. Then came the doubts about investigators' conclusion that it was an accident. 
 
 But the discovery that their son's body and skull had been stuffed with newspaper before burial added a horrific new dimension to their anguish and further fueled their skepticism of the official findings. 
 
 "We have been let down again," his father, Kenneth Johnson, told CNN. "When we buried Kendrick, we thought we were burying Kendrick, not half of Kendrick." 
 
 Kendrick Johnson was found dead in a gym at Lowndes County High School in January. State medical examiners concluded that the three-sport athlete suffocated after getting stuck in a rolled-up gym mat while reaching for a sneaker. 
 
 Death was not accidental, family's autopsy finds 
 
 His parents, Kenneth and Jacquelyn Johnson, never have bought that explanation. They won a court order to have their son's body exhumed and a second autopsy performed in June. 
 
 During an autopsy, internal organs are removed and examined before being returned for burial. But when Dr. Bill Anderson, the private pathologist who conducted the second autopsy, opened up the teen's remains, the brain, heart, lungs, liver and other viscera were missing. Every organ from the pelvis to the skull was gone. 
 
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 "I'm not sure at this point who did not return the organs to the body," Anderson said. "But I know when we got the body, the organs were not there." 
 
 Two entities had custody of Kendrick Johnson's body after his death -- the Georgia Bureau of Investigation, which conducted the first autopsy in January; and the Harrington Funeral Home in Valdosta, which handled the teen's embalming and burial. 
 
 GBI spokeswoman Sherry Lang told CNN that after the autopsy, "the organs were placed in Johnson's body, the body was closed, then the body was released to the funeral home." That's normal practice, Lang said. 
 
 The funeral home would not comment to CNN. But in a letter to the Johnsons' attorney, funeral home owner Antonio Harrington said his firm never received the teen's organs. Harrington wrote that the organs "were destroyed through natural process" due to the position of Kendrick Johnson's body when he died, and "discarded by the prosector before the body was sent back to Valdosta." A prosector dissects the body for pathological examination. 
 
 Scene points to foul play 
 
 Stuffing a body with old newsprint and department-store circulars -- "like he was a garbage can," as Jacquelyn Johnson put it -- isn't exactly standard practice in forensic pathology or the mortician's trade. Vernie Fountain, the founder of a Missouri embalming school, called it "not consistent with the standards of care" in the industry. And Dr. Gregory Schmunk, the president of the National Association of Medical Examiners, told CNN, "I have never heard of this practice." 
 
 Organs are typically placed in plastic bag, which is then put back into the body cavity after an autopsy, Schmunk told CNN in an e-mail. While individual organs may be kept back for further testing, he wrote, "This would not amount to all of the organs in any circumstance that I can imagine." 
 
 Funeral homes are licensed by the Georgia Secretary of State's office, which has opened an investigation into how Johnson's body was treated, said Jared Thomas, a spokesman for the agency. 
 
 Anderson, who was hired by the Johnson family for a second autopsy, found Kendrick Johnson had sustained a blow to the right side of his neck that was "consistent with inflicted injury." Challenging the state autopsy's finding of positional asphyxiation, he concluded the teen died as the result of "unexplained, apparent non-accidental, blunt force trauma." 
 
 And death scene imagery obtained exclusively by CNN has led a former FBI agent to question how Johnson died: "I think this young man met with foul play," said Harold Copus, now an Atlanta private investigator. 
 
 Lowndes County Sheriff Chris Prine refused to discuss the matter with CNN, calling Johnson's death a closed case. The U.S. Justice Department announced in September that it wouldn't open a civil rights investigation into the case. 
 
 But federal prosecutors in south Georgia have met with the family's representatives and are weighing whether to open their own probe, said Michael Moore, the U.S. attorney whose district includes Valdosta. 
 
 "This is about getting to the facts and the truth, and we want the Johnson family and the community of Valdosta to have confidence in the process," Moore said. "I am cognizant of time, and we continue to move the process along." 
 
 Moore urged anyone with information about Johnson's death to contact his office. Johnson's parents have come to believe their son's death was no accident, and the macabre discovery about their son's body has only deepened that belief. 
 
 "It's unbearable, just about," Jacquelyn Johnson said. "The only thing that wakes you up in the morning is to just keep pushing." ||||| See more disturbing developments in the Kendrick Johnson case on 'AC360" tonight, 8pm ET 
 
 Valdosta, Georgia (CNN) -- For the local sheriff's department, the death of 17-year-old Kendrick Johnson is a closed book: A tragedy, but an accident. 
 
 State medical examiners concluded that Johnson suffocated in January after getting stuck in a rolled-up gym mat while reaching for a sneaker. That's a finding his family has never accepted, and one challenged by the findings of a second autopsy they commissioned. 
 
 Now, death scene imagery obtained exclusively by CNN has led a former FBI agent to question how the three-sport athlete died. 
 
 Original story: Family demands answers in teen's death 
 
 "I don't believe this was an accident. I think this young man met with foul play," said Harold Copus, now an Atlanta private investigator. 
 
 And Johnson's father, Kenneth Johnson, said he believes authorities aren't leveling with his family. 
 
 "They know something happened in that gym, and they don't want it to come out," he said. 
 
 'Accidental' death challenged by new autopsy 
 
 A 15-minute video and nearly 700 photos taken by sheriff's investigators in Lowndes County documented the horrific scene. Johnson's body, clad in jeans and and layered orange and white T-shirts, was found wedged into a rolled-up wrestling mat in January. His face was bloated with pooled blood, some of which had poured out of his body, soaking his dreadlocks and spilling onto the floor. 
 
 There were more streaks of blood on a nearby wall -- but it wasn't Johnson's, according to investigators. Meanwhile, Copus said there appeared to be no blood on a sneaker that the teen supposedly was attempting to reach, located inches beneath him. 
 
 A pair of orange-and-black gym shoes found a few yards from the body had a substance that looked like blood on them, but investigators told CNN the stains weren't blood -- and so the shoes weren't collected as potential evidence. The same went for a hooded sweatshirt found a few feet away from the teen. 
 
 Copus said he can't explain how investigators handled items found around the gym. 
 
 Family: Kendrick's death wasn't accidental 
 
 "If you're running a crime scene, then you're going to say 'That's potential evidence. Obviously, we're going to check this out and find out who does it belong to,' " he said. 
 
 Lowndes County Sheriff Chris Prine refused to discuss the case with CNN, saying, "Our case is closed." But in June, an independent pathologist who conducted a second autopsy for the Johnson family found the teen suffered a blow to the right side of his neck that was "consistent with inflicted injury." 
 
 In May, sheriff's Lt. Stryde Jones told CNN that investigators tested the bloodstains on the nearby wall, "and it was not the blood of Kendrick Johnson." Investigators haven't determined whose blood it was, "but it doesn't appear to be involved in our crime in any way," he said. 
 
 "In the opinion of our crime scene personnel, after looking at it closely, the blood appeared as if it'd been there for an extended period of time. It didn't appear to be very fresh," Jones said. 
 
 But Copus said it's difficult to believe that old bloodstains weren't cleaned up. 
 
 "There is no way that they would allow whoever was supposed to clean this gym to leave that blood on that wall," he said. 
 
 In September, the Justice Department said it wouldn't open a civil rights investigation into Johnson's death. But federal prosecutors in south Georgia are reviewing the imagery to determine whether a separate investigation is necessary, the U.S. attorney's office in Macon told CNN. 
 
 For Johnson's father, the evidence is clear. 
 
 "Someone murdered him," he said. "They should be in jail." 
 
 Justice Department won't probe teen's death 
 
 Watch Anderson Cooper 360° weeknights 10pm ET. For the latest from AC360° click here.
– The plot has again thickened in the mysterious death of Georgia teen Kendrick Johnson: A second autopsy on the 17-year-old's exhumed body has found that before burial almost all of his organs were replaced with newspaper. Kendrick was found dead in a rolled-up wrestling mat at his school in January, in what was originally ruled an accidental asphyxiation. But his parents were suspicious and had him exhumed and examined by a private doctor. That doctor found evidence of "non-accidental" trauma, and now reveals that every organ from Kendrick's pelvis to skull—including his brain, lungs, heart, and liver—is missing, CNN reports. Newspapers were stuffed into the cavities the organs should have occupied "like he was a garbage can," his mother says. The Georgia Bureau of Investigation, which conducted the first autopsy, says it put all the organs back in afterward. But the funeral home that embalmed Kendrick tells the family's attorney that before it got the body the organs "were destroyed through natural process," and then "discarded by the prosecutor." The county sheriff, meanwhile, says the death is a closed case and refuses to discuss it. Yesterday, CNN revealed photos and video from the scene of Kendrick's death that raise serious questions about investigators' work, showing among other things blood stains on the wall that weren't investigated. "They know something happened in that gym," Kendrick's father says, "and they don't want it to come out." Click for more on the case.