It didn’t immediately occur to him that something far worse was wrong, it didn’t occur to him that his daughter hadn’t suffered an accident, but something intentional. It didn’t occur to him that this would be one of the last times he'd see her until his trial for her rape almost a year later.

According to his trial testimony, Mr. Lavigne went for his wife, Jamie, to get help. It was just after 7 a.m. and Mrs. Lavigne was finally drifting back to sleep again after waking up an hour or so before to take some pain medication. She ran some water in the bathtub and started lecturing her daughter about how to properly use the toilet. But the dark substance on her legs turned the water a bright red and they realized something was wrong.

Mrs. Lavigne asked her daughter, "did someone do something to you?"

"Daddy took me outside to the church parking lot," she told her mother. Mrs. Lavigne looked at her husband, who'd been standing in the bathroom doorway. He looked as shocked as she did. It was impossible, she thought, because she knew her husband had been asleep in bed with her all night, according to her own testimony.

Mrs. Lavigne asked her daughter again what had happened and she said "Daddy took me outside and put his pee pee in me." She turned to her husband and said "I think someone hurt our daughter," glancing over the fact that her daughter was calling that someone "daddy." To Mrs. Lavigne it was an off-handed statement from a hurt and confused little girl that had been through a traumatic—devastating— experience. She didn't give the notion of her husband as suspect a second thought, even when he bolted from the room.

He went to the kitchen, where he found their back door hanging open. He called out, asking his daughter if she'd left it that way. Yes, she had, she told her parents. It was how she came back in the house after being left alone outside.

They both teetered for a moment, unable to decide what had really happened and how serious the situation was, knowing that if they involved the police they'd have to admit to themselves that their five-year-old had been raped. "You know there'll be an investigation," Mr. Lavigne told his wife, and with that, called 911. What he didn't say at the time was that he knew he'd also be a suspect.

But unlike his daughter’s, Mr. Lavigne’s story never changed. Throughout the investigation and the 10 years he’s been in prison, he’s maintained his innocence.

But it was those words –"she says it was me"— that police immediately focused on and never let go of, it was those words that brought them to ignore a registered sex offender in the Lavigne's neighborhood and a mysterious red truck sitting outside their home that night. It was those words that made them believe they didn't need to fingerprint the doors in the Lavigne's house or even properly seal the crime scene before churchgoers could trample through it later that morning.

It was those words, and those words alone, that the state of West Virginia would use to convict Joe Lavigne of his daughter's rape and send him to prison for decades.

But then, at trial, those words never materialized.

But the jury never heard her words. They never materialized. The girl was only on the stand for a short time and her answers didn’t implicate her father, but at times, exonerated him. For example, when Barbera Allen, Mr. Lavigne’s attorney, asked where her father was while she was being raped, she told the jury he was “inside.�

At other times, she told the jury she didn’t know who had attacked her and as early as a few hours after the rape, her story changed from “my daddy� to someone who “looked� like her daddy. In the hospital, according to the testimony of the doctor that examined her, she said her attacker “had long hair, like my daddy used to have� and according to Mr. Lavigne's attorney, when interviewed by police months later, she said four separate times that she didn’t know who had raped her.

Ms. Allen told the jury in her closing argument that “(y)es, we know what (she) said right at the beginning. He’s (Mr. Lavigne) the one who made that public. He’s the one who did that. From then on, ladies and gentlemen, she has never said it again.�

And despite that Mr. Lavigne's daughter never implicated her father at the trial,  other witnesses seemed more than willing to fill-in the holes in the girl’s testimony.

The witness, the doctor who examined the victim in the emergency room, told the jury that “I asked her what happened, and she said that a man, and her quote was, ‘that looks like my daddy,’� had raped her, not that her dad himself had done it.

But then the doctor, without drawing any objections, added “but the inflection in her voice was, ‘if it wasn’t, he sure looked like my daddy.’�

Even the court reporter supplemented the girl’s testimony on the official record with her own observations, sometimes in ways that appear damaging to Mr. Lavigne. Take this exchange during the trial:

“…remember you told the Judge and Ms. Allen and everybody that you were going to tell us what happened. And we need to know, really, who did this to you? Do you remember?� Bill Rardin, the prosecutor, asked.

“I don’t know,� the girl replied.

Mr. Rardin tried again. “You don’t know? Have you ever seen him before?�

Then, the court reporter wrote “(w)hereupon, the witness turned slightly in chair and looked at the Defendant.� None of the other officials in the courtroom, the judge or the attorneys, noticed that the girl had "turned slightly" or asked that the record be marked with the girl's movements.

It’s not unusal, according to Carol Tavris, for juries to convict suspected child abusers on razor-thin evidence. A social psychologist in Los Angeles and advisor to the National Center for Reason and Justice (NCRJ), an innocence project specializing in those falsely accused of child abuse, she told Where Doubt Remains that juries are so afraid of the possibility of putting a pedophile back on the street, that they’ll forgo logic and the standards of proof required for criminal convictions.

“They would often rather put an innocent person in prison than take that risk,� she said.

And when it comes to police and prosecutors who refuse to abandon early theories of crimes that aren’t supported by evidence, she says that there are “those who blind themselves to the possibility of error … when you put the words ‘child’ and ‘sex abuse’ in the same sentence, a lot of people lose their critical faculties.� Ms. Tavris co-authored the book Mistakes Were Made (But Not By Me) in which she argues that self-justification blinds most people to the possibility of error, police and prosecutors no exception.

On the board of NCRJ and author of Victims of Memory: Sex Abuse Accusations and Shattered Lives, Mark Pendergrast told Where Doubt Remains that "people jump to conclusions and they leap to an assumption of guilt almost immediately, more than any other form of crime." Once accused himself by his daughters after they underwent therapy that helped them recover what they believed were repressed memories of childhood sexual abuse, Mr. Pendergrast says there's a "witch-hunt mentality" in the country that started with daycare panic cases in the 80s and continues today.

But it’s not a surprise or even unusual that the police focused on Joe Lavigne as a suspect, at least, at first. He readily admits that his daughter spontaneously and without leading accused him of rape. But in a letter to Where Doubt Remains, he wrote “I am not a child rapist. I did not rape my daughter. The man who did got away because I was the only one the police and the prosecutor would look at.�

“In working sex crimes you always try to identify if you have any sex offenders in the area,� a private detective and former State Police trooper working for Mr. Lavigne's defense, told the jury. He discovered the man and passed his name and address on to the Hurricane Police Department, which was investigating the rape. But Ron Smith, the lead investigator on the case, said at trial he never received the information.

Still, Mr. Smith testified that he did review the State Police’s sex offender registry –which would've had the man's name and address on it— but that he did so "well after the fact.� He told the jury that when he saw the list of sex offenders living in the Lavigne's County, nothing jumped out at him and he didn’t follow-up on any of the names.

The man, meanwhile, still living near Hurricane, told Where Doubt Remains that he didn't know anything about the Lavigne case—at first. When pressed, he later admitted to knowing about the family, but only from news accounts he'd heard nearly a decade ago.

He confirmed that police never spoke with him and then offered that he'd always lived "13 or 14 miles" from the Lavigne's house on Teays Valley Road, contradicting the private investigator's sworn testimony, public records and his former neighbors.

When asked how he knew where the Lavignes had lived when he only remembered them from news reports, he wouldn’t answer.

Mr. Rardin, in his closing argument, told the jury that the man “in no way matches the description (the victim) told you,� and earlier, “Don’t sit back there and say ‘I wonder if that guy did it.’�

He also denied that the police ignored any suspects. “You saw Ron Smith. You saw him with that little girl and if you believe for one second that if he knew somebody else did this or had a lead he wouldn’t try to find the person that hurt (her) … to insinuate that he would let a rapist loose on the street would be just not believable.�

Mr. Rardin didn't respond to requests for comment and Mr. Smith's new chief (he now works for the Winfield Police Department) declined to allow Mr. Smith to comment about his work on the Lavigne case.

Police also failed to fingerprint the front and back doors of the Lavigne home, despite multiple requests to do so from Mr. Lavigne and his wife. One of the doors, which the Lavignes said in court they never used, was found propped open by a brick the morning Katie Lavigne was raped. The other door was freshly painted the day before the rape.

Mr. Smith told the jury he didn’t think it was necessary to fingerprint the doors and that he didn’t feel any usable prints could be taken from one of the door handles, because it was porous, grooved and ridged. Ms. Allen, however, had the door handle removed and brought to court.

Showing it to him, she asked “Now that’s as smooth as can be, isn’t it?�

“If that’s the exact one,� Mr. Smith answered.

“I’m representing to you there will be a follow-up that this is it. This was taken right from the door. My question is, this place where you would put the thumb to pull open that door, that’s as smooth as can be. Correct?�

“Yes, that’s fairly smooth," he said.

Other witnesses reported seeing a red truck in the parking lot by the church early the morning of the rape. Mr. Smith looked into the truck, which he admitted had no reason to be in the parking lot at that time—but stopped short of finding out who it belonged to.

Mr. Smith told the jury “the truck was seen at three-thirty (3:30) a.m. and it was also seen at four-thirty (4:30), and then when the daughter went to bed at five-thirty (5:30) she thought the truck was still there.�

“So at five-thirty (5:30) a.m. on February 11th, 1996, this unidentified red truck was still sitting here in the parking lot?� Ms. Allen asked.

Under questioning from Ms. Allen, Mr. Smith said he ruled out any legitimate reason the truck would’ve been in the parking lot.

“And, in fact, you just don't know whose red truck that was, do you?� Ms. Allen asked.

“No. I don't,� Mr. Smith answered.

At trial, though, Mr. Smith pointed out the things he did that showed he was intent on discovering who raped Mr. Lavigne's daughter, like extensive searches for the victim's clothing (they've never been found) and a BOLO alert (be on the look out) to nearby police agencies. He also denied that he was ever asked to seal the crime scene.

(CLARIFICATION 12/19/2007 at 1:30 p.m. | after reading this article, Mr. Ayers contacted Where Doubt Remains to reiterate that while he firmly believes the victim mistook her attacker for her father, he, at the time, didn't feel that the sex offender known to have lived near the Lavignes looked much like Mr. Lavigne. His judgment was based on pictures and since his interview with Where Doubt Remains, he has seen other photos from different time periods and now feels that Mr. Lavigne and the man do have many physical similarities).

Mr. Lavigne, however, has called into question the credibility of the state trooper doing the tests, Howard Brent Myers. Not long after Mr. Lavigne’s case was over, a federal magistrate issued a scathing report accusing Mr. Myers of lying on the witness stand in an unrelated rape case in the late 80s and early 90s. The magistrate said Mr. Myers "falsely testified about nonexistent serology test results supposedly linking (the defendant) to the crime,� noting that the lab didn’t even have the equipment required to perform the test Myers claimed to have done.

Mr. Myers subsequently told the court that he mistakenly referred to the wrong tests, and hadn’t meant to mislead anyone. He said he was following a policy established under his by then-disgraced colleague, Fred Zain. The State Supreme Court invalidated all of Mr. Zain’s testimony in West Virginia in 1993, after an investigation revealed that he had for years manipulated test results to implicate defendants and then lied about it at trials.

According to news reports, after Myers’ false testimony was discovered, the Zain investigation was reopened to see if any others in the lab had lied about performing tests. It’s unclear where that investigation went and the State Police say they're having trouble locating Mr. Myers' reports from the Lavigne case. The State Police public affairs office didn't respond to requests for comment from Where Doubt Remains.

Still, even without the questions surrounding Mr. Myers credibility, one expert sees other reasons to have the evidence in Mr. Lavigne’s case retested. Dr. Jeffrey Wells, chair of WVU’s Biology Department and an expert in forensic biology, reviewed Mr. Myers’ testimony and he told Where Doubt Remains that even if the lab really couldn’t find DNA 10 years ago, new tests today might.

He said that technology has considerably improved, especially in the area of DNA testing, and that forensics experts now use techniques that can more readily target male biological material like sperm, even in minute amounts.

The doctors who performed the victim's rape kit may have also further complicated things by unwittingly destroying and tainting evidence, according to a leading academic urologist in the state.

He reviewed the rape kit procedures used on the victim and told Where Doubt Remains that the doctors probably diluted the samples so much that finding DNA in later tests would've been difficult. Instead of using a lavage as the doctors did, which involves washing the victim with a saline solution and then collecting the solution for testing, the urologist said he would've attempted to collect dry samples from the girl's wounds with swabs.

Mr. Ayers is also cautious. He told Where Doubt Remains that there's no guarantee that there's any evidence still available for testing and he noted that doctors testified to collecting some samples in the rape kit that somehow never made it to the police lab for testing. Even Mr. Myers testified that he simply chose to not test some of the samples, because he didn't feel they'd reveal any useful information.

Still, Mr. Ayers he's not ruling out avenues for investigation, including seeking new DNA tests. He wouldn't say, however, if his office is considering claiming that Mr. Lavigne's trial attorney, Ms. Allen, now a deputy attorney general, was ineffective. "She's a good attorney. I think she did what she thought was best for Joe," he said. But he also pointed out that his office isn't at the point in its investigation where they've settled on a legal strategy or are ready to file any court documents, noting he's the sixth or seventh public defender that's been assigned to Mr. Lavigne's case since he was convicted.

But he's hopeful, along with his investigator, that Mr. Lavigne will someday be exonerated. "We believe in Joe's innocence," he said.

Michael’s confession wasn’t a surprise. For weeks after his return home his mother had been telling him that “he had to tell the truth� and that “he needed counseling� because of “what happened to him� at the hands of the friend, Lee Jones.

She was suspicious, she’d later tell police, not because a grown man wanted to take a 12-year-old to the beach alone nor because Michael acted any differently after returning, but because of rumors she’d heard that Mr. Jones had “messed with� other boys in a tiny, isolated town in West Virginia called Gauley Bridge. Mr. Jones lived there and up until a few months before the beach trip, so did Michael.

According to Michael, the questions from his mother started the minute he returned home and didn’t stop until he confessed that Mr. Jones had fondled him and forced him to have oral sex in their hotel room.

And while Michael’s mother seemed anxious to know if anything had happened to Michael, it’s difficult to piece together how long she waited before telling anyone. The trip was in late June, but social services in North Carolina didn’t launch an investigation until the middle of October, after receiving a report from a counselor at Michael’s school (Mrs. Roop later told a state social worker she’d reported the allegation to his counselor a few weeks before). A social worker interviewed Michael and his mother and as required by law, reported the allegation to the police.

From there, the case was assigned to Len Sloan, a detective in Myrtle Beach who said at trial that he had no experience investigating sex crimes or child abuse claims. His case notes show he had trouble pinning down details in Michael’s story and he never interviewed Michael because his department wouldn’t pay his travel expenses.

But still, when a prosecutor in Myrtle Beach expressed doubt about Michael’s claims and whether they had enough evidence, Mr. Sloan assured him that other people found the boy to be credible (the social worker, for example, told Mr. Sloan he believe Michael’s claims). He then pressed for a court order to bring Mr. Jones back to Myrtle Beach to face charges.

Meanwhile, in Gauley Bridge, the West Virginia State Police were busy building a case of their own. Within days of learning of Michael’s accusation, they located nearly a half-dozen other witnesses–mostly young men—also claiming that Mr. Jones had raped them. By the time he was arrested in early February, 1998, police had located just under a dozen accusers with claims of sexual abuse spanning nearly fifteen years.

The scandal rocked Gauley Bridge, dividing friends and neighbors. The story gained statewide coverage and after Mr. Jones’ eventual conviction, wire stories about the case were picked up by the New York Times and the Washington Post. And while the media put the high-profile case under an intense light, there are few indications that reporters ever questioned the weight of the evidence that was mounting against Mr. Jones.

Many Gauley Bridge residents did question the evidence, however. Mr. Jones was a well known figure in town, but not just because he was only one of about 750 living there, but because he was also their chief of police.

In West Virginia, that’s largely okay. Courts here will generally instruct juries that they can find a defendant guilty without any corroboration of the victim’s story when it comes to sex crimes. Still, the prosecution is required to prove the charges and the police are expected to, at the very least, make sure there is some truth to the allegations.

In the case of Lee Jones, that didn’t always happen. After a nine-month investigation by Where Doubt Remains that included a review of thousands of case documents, video and audio tapes and dozens of interviews, what follows is the first in-depth look at why Lee Jones’case and why his guilt should be doubted—starting with the grand jury.

Charges dropped, but new ones added

In the spring of 1998, Special Prosecutor Kristen Keller and then Sgt. Scott VanMeter of the State Police presented 53 charges against Mr. Jones to a Fayette County grand jury, six or seven of which they said occurred from 1983 through the middle of 1985. Then, they found out Mr. Jones didn't move to Fayette County until July 1985.

Instead of going to trial without the first six charges –which happened to part of a group of more serious crimes Mr. Jones was charged with—transcripts show that Ms. Keller went back to the grand jury to get a new indictment. But this time, in place of the earlier charges she could no longer bring against Mr. Jones, Ms. Keller added at least six new charges after 1985 to coincide with his arrival in the county. Mr. VanMeter explained, according to a transcript of the proceedings, that simply, "The dates were off..."

The first grand jury was told that the state wasn't charging Mr. Jones with all the crimes they believed he committed, which could explain where the new charges the state added with the second grand jury came from. But, still, the defense argued at a pretrial hearing that the morphing indictment violated state law and even the state constitution--noting that the second time around, Mr. VanMeter didn't present any evidence to support his claims, particularly, the new ones the state added post-July 1985.

But the judge decided that Mr. Jones' attorneys waited too long to complain, and the trial went forward on all charges (by then, there were 54). The state presented its case first, with a 14-year-old boy who had a history of making abuse claims and then backing away from them as their star witness.

“She’s had things against Lee…� Michael told the attorneys, according to a transcript of his deposition. “He put her in a mental home,� referring to an incident in which Mr. Jones, responding to an emergency call, found Michael’s mother on her balcony, naked and screaming hysterically. She was taken away in an ambulance and later involuntarily committed by her husband to hospitals and treatment centers for six months.

According to the deposition, Michael’s mother fed him details of sexual abuse that he believed she had suffered herself as a child, and told him to repeat them when questioned by the police and at trial.

Michael told the attorneys that he came to them because he wanted to finally tell the truth. “I just—I just knew it was wrong after I sat here thinking about it for a long time. I was sitting thinking about it after it happened , and I realized it was wrong, and I didn’t know what to do…� he said, according to the deposition transcript.

Ms. Keller points out, however, that Michael’s story didn’t change until he was returned to West Virginia to live with his father—a friend of Mr. Jones and a man Michael accused at trial of beating him. She told Where Doubt Remains she’s neither surprised nor swayed by Michael’s sudden reversal.

“We look at recantation as just another part of prosecuting a case,� she said. “As a child witness, it’s something we’d expect,� again pointing out that Michael was now in what she believed was a “closed environment.�

But Michael’s also taken back the allegations he made against his father, saying in the deposition that his mother forced him to make those up, too (not to mention that none of the adults in his life, including his teachers and principal, ever saw him with the “blackedâ€? eyes he claimed at trial his father gave him at least once a month for years).  And there is other evidence to suggest that Michael’s story wasn’t his own.

On it, Mr. VanMeter asks Michael if he knows of any other boys that Mr. Jones may have abused.

Michael answers “I think,� and then turns to his mother, who is sitting behind him on a couch. “Mom, didn’t you say my cousin Adam?�

“I didn’t say. You did,� Mrs. Roop answers.

“Somebody said,� Michael replies, “you said that they visited Adam because Lee did this to Adam, too, didn’t you?�

“I didn’t say nothing,� his mother says.

“Uh-huh, because you were talking about—“

“Just answer his questions,� she snaps, cutting him off.

A red truck

In addition to arguing with his mother about where the information he was giving police came from, Michael also got some details key to the state's charges against Mr. Jones wrong.

At trial, Michael told the jury that in 1996, Mr. Jones molested him in a red, Dodge Ram truck that he had recently purchased. The state indicted Mr. Jones for raping Michael in that truck, but according to the title documents, the truck wasn't purchased until just a few weeks before Michael left for North Carolina—in 1997. Ms. Keller told the jury that Michael was probably wrong about the red truck. She suggested that Michael's age made it difficult for him to remember exact details.

However, when it came to Mr. Jones’ cars, Michael was something of an expert. At trial, he accurately recalled the year, make and model of each vehicle Mr. Jones owned since the two had met in the early 1990s. On the taped interview he did with Mr. VanMeter, he's sure of the details--noting that Mr. Jones often let him drive his cars when the two were alone.

None of it mattered to the jury, though. They still convicted Mr. Jones for raping Michael in a truck that he didn’t own.

The truck wasn't the only thing that Michael got wrong. During the investigation, he told the police, at least according to police reports and affidavits, that he and Mr. Jones stayed on the fifth floor—room 505—of the Tropical Seas South, a motel in Myrtle Beach (at trial, he denied ever telling the police that). But Michael never stayed in room 505.

Still, according to records from the Myrtle Beach police department, Michael told police he had stayed in room 505. Mr. Sloan, a detective in Myrtle Beach, told the jury he checked out Michael’s story and found evidence to support it – receipts from the hotel showing that Mr. Jones stayed in room 505 that summer. He told the jury that the receipts “corroborated� Michael’s story.

But really, they didn’t. The receipts note the trip was for one night, Michael told police he and Mr. Jones stayed through a weekend; the dates of the booking are a Monday and Tuesday in August, Michael and his mother had both previously said it was a Friday and Saturday in late June or July; the receipt lists three adults on the trip while Michael had told police he was alone with Mr. Jones.

Now, Mr. Jones has never denied taking a trip with Michael to Myrtle Beach that summer, but despite what Mr. Sloan told the jury, the receipts clearly don’t “corroborate� Michael’s story and what’s more, Mr. Sloan likely knew that when he testified.

His case notes from December 1997 indicate he was told there was a problem with the dates. He went to the trouble of having Michael interviewed again in January 1998 to clear things up, but this time, according to Mr. Sloan’s notes, Michael was less sure than before about how many nights he had stayed in Myrtle Beach.

The prosecution also noted at trial that at one point, Mr. Jones had planned to bring another adult on the trip and that the receipt, if it was assumed to indicate the number of guests book as opposed to the number stayed, would’ve supported Michael’s story. However, all testimony at trial and all police reports are consistent on one point about the hotel – Mr. Jones didn’t arrange a room for the trip with Michael until the two were already in Myrtle Beach, after it was clear it would only be the two of them.

The jury never heard about Mr. Sloan’s trouble nailing down the dates of the Myrtle Beach trip, or why Michael reported the room number of trip he wasn’t on. Neither did the South Carolina judge who issued an arrest warrant for Mr. Jones based on an affidavit from Mr. Sloan that said “the boy reports…they stayed in room 505.�

Mr. Sloan didn't respond to questions about his testimony and the affidavit, neither did officials in the Myrtle Beach police department.