The central Florida man is more than two decades into a 70-year sentence for aggravated child abuse. He was convicted of the crime after he and his wife brought their infant son Kody to the emergency room in 1993 when they noticed he was in pain and not using the left side of his body.
The doctor found 13 broken bones and a skull fracture in his X-rays but no bruises. The hospital called police.
"I am innocent," Duncan, now 51, told CNN. "I did not harm my son."
Prosecutors are standing by the conviction, but Duncan said he hopes a new lawyer, and new medical science, will end his nightmare and bring him home.
Duncan and several family members, including his ex-wife and Kody Duncan, who as an infant was at the heart of the case, sat down to tell their story in the CNN Special Reports' "Broken Bones, Shattered Lives" that airs at 8 p.m. ET Saturday.
"All I could think about was, 'Oh, my God, he's gonna die in there and never see his kids,'" said Jim Duncan's mother, Celeste Bonnell.
So far, she has been right. His two boys, Kevin and Kody, are now men in their 20s. Kody's bones healed, and he said he believes his father was wrongly convicted.
"I never once had a doubt that he hurt me. I don't believe it," Kody said.
Defense: 'A case of a wrongfully convicted man'
Prosecutors leaned heavily on medical testimony -- from Florida pediatrician Mark Morris, who still stands by his findings -- and the X-rays.
One key witness, the grandmother of Duncan's then-wife, said she saw him harm his son and even demonstrated in a police video what she saw firsthand to law enforcement, but she later recanted and her statement was not used in the case.
Kody's mother, Ronda Duncan, said the investigation threatened to tear the family apart.
"From the beginning they wanted us all to just be like vultures and go after each other. It turned extremely ugly, very, very ugly."
Jim Duncan and his supporters contend his conviction stems from a rush to judgment.
According to court transcripts, Kody, then 2 months old, had fractures of his arm, both legs, multiple ribs, clavicle and skull, leading authorities to believe he was a victim of vicious abuse.
"It's a bad diagnosis," Illinois radiologist David Ayoub contends 20 years later.
He said he believes Kody had infantile rickets, a disease of early life in which bones do not mineralize properly. Ayoub said it led Kody to develop metabolic bone disease, causing his bones to be very fragile.
Ayoub said babies with the disease have bones so fragile that even regular handling can cause breakage. And those fractures, he said, are often misdiagnosed as abuse.
With that diagnosis, Florida defense attorney Lisabeth Fryer is working to get Duncan's conviction overturned.
The goal: "Hear the testimony of the doctors, learn about the new diagnosis, and the new science, grant Mr. Duncan a new trial," Fryer said. "This is a case of a wrongfully convicted man. There is no victim. There is no crime."
Battle of the medical experts
But the case could come down to a battle of the medical experts.
After looking at a copy of the X-rays, Dr. Peter Strouse, director of pediatric radiology at C.S. Mott Children's Hospital in Ann Arbor, Michigan, told CNN the findings were consistent with child abuse, saying there was no evidence of bone disease.
But the family is overjoyed that Duncan will finally get a new day in court to say he is innocent and that a crime was never committed.
They've gained new hope now that the Florida 2nd District Court of Appeal has ordered that he will have a full evidentiary hearing for a new trial in 2018.
Duncan said if he gets out it's important for him to be able to hug his sons, especially Kody.
"I just remember always praying, 'God let me out before they turn 6, before they turn 8,' " Duncan said from the Avon Park Correctional Institution in Highlands County, Florida. "I wanted to have some of their childhood."
As a child victim under the law, Kody Duncan wasn't able to visit his father in prison, but the two have remained close, sharing two phone calls every week.
Authorities still view him as a victim, prohibiting visits between father and son.
Now a Pinellas County, Florida, court will weigh whether a new trial is warranted to determine if Kody was a victim of abuse at all.
"I wish I could talk to him in person," he said. "I just wish I could see my dad."