WATCH: Judge finds 14-year-old Jordan guilty of murdering woman, her unborn child: Part 5

WATCH: Judge finds 14-year-old Jordan guilty of murdering woman, her unborn child: Part 5

Transcript for Judge finds 14-year-old Jordan guilty of murdering woman, her unborn child: Part 5

For the family of the victim, there’s pain in Jordan brown denying he shot Kenzie Houk in the bed as she slept. She was 8 1/2 months pregnant. Reporter: It’s been three years since Jordan brown entered this Pennsylvania detention center. So long that there’s now a new prosecutor on the case. Chris brown hasn’t stopped hoping the scales of justice will finally tilt in his son’s favor. He has total faith in both of his attorneys and he believes he is going to eventually come home. Reporter: But if Pennsylvania investigators have their way, it will be years before Jordan brown tastes freedom. There is not a trooper on scene that day that has lost one second of sleep over this case. Reporter: In a murder trial that barely lasted three days, the case is decided by a jury of one. Judge John Hodge. Once you have a bench trial, it’s one person who’s making that decision. Reporter: Judge Hodge’s verdict, swift and severe. Jordan brown, by then 14 years old, guilty of double homicide. And pray that somehow today — The Houk family’s prayers were answered this afternoon when a judge announced a guilty verdict. Reporter: It’s a stunning gut-punch for Jordan brown and his legal team. I can remember when he announced that verdict just looking at Jordan and feeling like we had failed him. And just feeling so sorry for him at that moment. Reporter: But still convinced Jordan brown is innocent, his lawyers vow to take their fight all the way to the supreme court of Pennsylvania. He lost his childhood on a false conviction and he needs to be exonerated. Reporter: Jordan’s lawyers begin picking apart the prosecution’s case. Starting with that youth model shotgun that authorities say smelled like it had recently been shot. Those law enforcement officers who said that they smelled it was recently fired, they conceded that they had no expertise or training. Reporter: And yet they dubbed it the smoking gun. Correct. They dubbed it the smoking gun. Reporter: You arrested an 11-year-old boy based on the smell of a recently shot shotgun and a shell casing that was found after he was arrested. And someone who was within feet and heard the blast. Reporter: Remember, that someone was Kenzie’s older daughter Janessa, but it turns out the explosive statement she gave police, where she said she heard a boom right before they left for school, that bombshell was never entered into evidence at trial. Janessa never testified. Does it occur to you that maybe they didn’t enter it into evidence because it wasn’t reliable? No. No way, shape, or form. You’re talking about a 7-year-old taking a stand in a courtroom. It had nothing to do with her being unreliable. All they really arrested him on, largely, was the statement of Janessa. As time went on they completely abandoned that statement, which would have been the strongest evidence in the case, and rather tried to pursue a prosecution based upon this forensic evidence. Reporter: But the forensic pickings are slim, starting with the shell casing they claim Jordan tossed on his way to the school bus. On that property where they lived on a farm, there were shotgun shells all over the place. They routinely shot on that property. The discovery of that shell was not significant. Reporter: And police were never able to prove Jordan’s shotgun was the murder weapon. All you can really say is it was this type of gun, but you can’t definitively say it was this gun. Reporter: Also curious is the fact that there was no blood or tissue, also known as blowback, found on Jordan’s gun. The absence of any tissue or blood on his clothing, on the barrel of the gun, it’s almost inconceivable that you could suggest that a shotgun was fired at close range, and it wouldn’t deposit any tissue, any blood on the barrel of the gun or on his clothing which he wore to school. It was appalling to me that they seemingly just ignored that fact throughout the case. Reporter: But the prosecution’s expert testified that the angle at which the gun was shot could have minimized the blowback. And the police have their own theory. Our theory is that the blowback would have been stopped, most of it, if not all of it, from the hair of Kenzie. Reporter: You think hair would stop the blowback of a shotgun blast? Between the hair and the fold in the skin with the direction it was pulled back, yes. Reporter: But these seasoned investigators, who admit they rarely work on murder cases, insist they have the goods on Jordan brown. Why did you arrest him at 3:30 in the morning? Because we wanted to do a search warrant on his clothes also. Reporter: And what did you find on his clothes? They discovered gunshot residue and gunshot particles on his shirt and pants. Reporter: The defense argues that gunpowder came from a jacket Jordan wore at a Turkey shoot days earlier. And the prosecution’s own expert said it was just as likely those two particles of gunshot residue could’ve transferred to Jordan’s clothes. Which leaves Jordan’s legal team with one big question. Where is the physical evidence? In order for this perfect storm of a crime to have happened with the 11-year-old as the trigger man, what would have had to take place? This is precisely what would have had to have happened. Jordan brown was sitting with his stepsister Janessa in a room adjacent to the room where the victim was sleeping, run upstairsgrab a shotgun, load it with a shotgun shell. Walk over to the bed, place that shotgun up against her head, pull that trigger, kill her, somehow manage to wipe whatever bodily fluid or blood might have been contained on the end of that gun, take it upstairs, replace it along the wall. Remove the shell, run downstairs while her sister presumably was waiting for him. All without leaving a single clue. Reporter: And Jordan’s lawyers say the police timeline means it all happened within a couple of minutes. An 11-year-old child can’t make a peanut butter and jelly sandwich and drink a glass of milk without leaving clues. Reporter: And tonight, a brand new witness. Kenzie’s younger daughter, adalynn, now 13. Coming forward with an account that flies in the face of the police timeline. Mother, you fill my life with happiness and my heart with love. The gunshot was what had woken me up. I was so young. I did not know what the sound was. I was just gonna walk in to wake her up. And her phone rang. I went and answered the phone. And I was like, “Hi.” And they were like, “Can I talk to your mother?” I went in to wake her up. And her face was facing me. I was just like, “Hey, mom, wake up.” And when I turned her over, I realized. So I hung up the phone and went outside. Reporter: A treetrimmer spots adalynn sometime after 9:00 A.M. If you go according to adalynn’s recollection, Jordan and Janessa would’ve have been long gone on the school bus when Kenzie was killed. And I just sat there and cried with my little blanket. Reporter: Her family says adalynn shared bits of her story over the years, but it’s something neither police nor Jordan’s defense team have ever heard. His lawyers say her timeline means Jordan wasn’t there, but we asked an investigator to respond, who says after so many years he finds her account not credible. So this is the casing? But if the timeline falls apart, what about the forensics? Did you ever check his hands for gunshot residue? We did not. Reporter: Can you tell me why no one dusted for fingerprints on the unlocked doors? I don’t know if it wasn’t done. Reporter: It was never reported. ‘Cause when this initially happened, they didn’t know what it was and they were gonna try to save her. And they actually try to save her to give her cpr. Reporter: So a bunch of people went in and out. Yes. Reporter: So you’re saying the crime scene was contaminated? The door. Reporter: So you never got fingerprints off the door? No. And we fingerprinted a gun, there was no fingerprints on the gun either. Fingerprints are very hard because you need a very perfectly good fingerprint that wasn’t moved when it touched something. Reporter: Fall, 2017, more than eight years after his arrest, Jordan brown’s legal team will finally have their case heard by the supreme court of Pennsylvania. I pray this never happens to

This transcript has been automatically generated and may not be 100% accurate.

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