Into Thin Air

Produced by Brian Leonard, Daria Hirsch, and Sara Ely Hulse

This story originally aired on Oct. 18, 2008. It was updated on June 20, 2009.

When Jean Zapata vanished from her home in Madison, Wis., in 1976, she left behind her daughter Linda, two other children, a lot of friends, and a mystery that would take more than 30 years to solve.

"I spent my whole life from age 11 just telling people when they asked, 'My mom abandoned me,'" Linda remembers.

She only knew what her father had told her when on the day her mother disappeared. "At age 11, when my dad said she took off because she was stressed out, it was cemented in my head. She took off and she's raising another family somewhere."

Had Jean really taken off and left her family and friends behind? As Richard Schlesinger reports, a set of new detectives would take a fresh look at the case decades later, and try to solve the question everyone wanted to know: what really happened to Jean Zapata?

A lifetime of nagging questions and haunting memories would bring Peggy and Jean's daughter Linda together. Neither could have predicted it, but digging for the truth would involve terrible choices and betrayal.

It all started in Madison in the early 1950's, when Peggy and Jean first became best friends. Peggy was with her best friend for all the good times, including when Jean married a promising engineer, Eugene Zapata. They had three children: Christine, Steve and Linda.

Eugene went to work for the Department of Transportation, but Jean was no stay-at-home mom: once the kids were in school, she returned to her other love, flying, and became one of the few female flight instructors of her day.

But at home, not all was well. According to Peggy, Jean was happy in her marriage with Eugene for the first half of their time together. It became one of those marriages where behind closed doors, there was trouble.

"She told me that they were having problems in the bedroom, but she didn't go into any detail at all. She seemed to think that he had a lot more testosterone before she said 'I do.' But we didn't talk about that a lot. After all, we were nice girls. And nice girls didn't have problems with their marriage," Peggy says.

Jean wanted to keep the spark alive, even if it meant agreeing to do things nice girls didn't always do. But no matter what she did, nothing worked. In May 1976, about 17 years after they married, Jean filed for divorce.

Eugene moved out of the house and Jean began to explore life as a newly single woman. Before long, she met Paul Lee, and they had an instant connection. Jean and Paul talked every day, but the relationship didn't last long.

On Monday, Oct. 11, 1976, Linda remembers seeing her mother drinking her morning coffee. "She was in the kitchen and I was looking down the foyer hallway. And I was leaving for school. And I just caught a glimpse of her in the kitchen as I was shutting the door and I took off for school."

Linda never saw her mother again.

Ivan Norton worked with Jean at her flight school, and was surprised when she did not show up to teach a student pilot that day.

At the house where Jean and the kids lived, Eugene was already explaining to his children where their mother was. "I asked, 'Where's Mom?' And he said, 'She probably needs a break or a vacation. And she'll probably be home in a couple weeks,'" Linda remembers.

When Jean didn't show up for work after three days, Ivan called the police and then called Eugene. "I says, 'Well, hey, have you turned in her missing to the police?' 'No, I haven't done it.' And I said, 'Well, you don't have to. I did,'" Ivan recalls.

A week after Jean went missing, Police Officer Greg Martin showed up at the Zapata house. He was just trying out for the detective squad, so he was assigned what had been classified as just a routine missing person case. "I went in and I noticed there was no damage, no evidence of a fight, no evidence of a struggle or anything that we could see. The first thing I noticed that was totally out of order was that her purse was there," he remembers. "A woman goes nowhere without her purse."

Officially, Jean was classified as a missing person by the Madison, Wis. police department. But Officer Martin noticed something strange about Eugene's behavior following the disappearance of his estranged wife. "He was like a blank sheet of paper. I mean there was nothing on him to read and that bothered me," he remembers.

Martin says he asked Eugene to take a lie detector test, and he agreed. Eugene passed the test, but investigators thought there was something unusual about his demeanor.

Martin says he was unable to get under Eugene's skin. "I thought realistically that by pushing him into a lie detector test that I would get some movement. I got absolutely nothing."

His only other possible suspect, Jean's boyfriend Paul Lee, took and passed his lie detector test and was cleared of any suspicion.

But police were learning some things about the Zapatas' marriage, which added to their suspicions. "Eugene had placed an ad for her in a swingers type magazine," Martin explains.

One day the post office called Jean to complain about x-rated material in a mailbox rented by Eugene. It was the first she'd heard about the mailbox. So she went to look and was horrified by what she found. "She picks it up and is rifling through it, and she sees her own nude picture looking back at her where her husband is pimping her out to anyone who subscribes to that magazine," Peggy says.

Remember, this happened when Jean was still trying to save her marriage. "At one point, when Eugene said he just didn't seem to have any lead in his pencil, but it might help if he could take provocative pictures of her, she let him. Never realizing that years later, these pictures would come back to haunt her," Peggy says.

Jean's divorce attorney, Daphne Webb, learned that the swingers' magazine was only part of the story. "They would go to bars and he'd want her to stand off to one side so that he could pretend that she was a pickup and see if men would try to pick her up. I think most disturbing to her was that he would kind of reach up under her clothes and grope her when the children were present."

Jean not only wanted a divorce, she wanted a restraining order.

Eugene moved out, but he didn't move on. The divorce was bitter, and he seemed obsessed with Jean. "In today's terms I would say she was describing stalking behavior. He would come to the house on the pretext of seeing the children and he would go through her underwear drawer and her possessions. And she found it very disturbing," Webb says.

The restraining order limited Eugene's visitation rights with the children to 9 a.m. and 11 a.m. on Saturdays. That's the only time he was permitted to be at the house.

On the Monday morning that she disappeared, Jean telephoned her attorney at about 8:15 a.m. and left a message. When Webb returned the call about an hour later, it was Eugene who answered. "Which was surprising because he was not supposed to be in the house," Webb points out.

Asked what she said to Eugene, Webb says, "Well, I said, 'I'm returning Jeanette's call.' And, he said, 'Well, I don't know where she is.' Her car is still here.' I think he said her purse was still on the table, and I didn't suspect any foul play… So, I just said, 'Well, I returned her call. Let her know when you see her.'"

Webb told police all that at the time, but there was no physical evidence of foul play.

And after just three weeks, the case went cold. Eugene moved back into the house, and for Linda, it was as if her mother had simply never existed. "It's really odd, but somehow, no one talked about it. No one brought her up. I don't think I used the word 'Mom' until I was in my late teens, early 20s. I don't know why," she says. "Back then it was so taboo. And no one told me not to talk about it, but the three of us kids, I think we all just shut down. For me, there was this enormous uncomfortable elephant in the middle of the room. And no one talked about it."

Two years after Jean disappeared, Eugene married his current wife Joan. Linda now had a stepmother, but she still waited and hoped her own mom would return.

Years and decades passed, and the Zapata children grew up and moved out.

Peggy moved away from Madison, but she never forgot about her best friend.

In November 2004, more than 28 years after Jean disappeared, Peggy decided there was something she had to do for her friend. So she contacted the Madison Police Department to see if they had a Cold Case Squad.

They didn't, but the case landed on the desk of Det. Marianne Flynn Statz. Asked what she thought when she read the case, Statz says, "I immediately was struck that more could probably be done with the case.

The detective didn't believe Jean had simply run away, as her husband had claimed for the last 28 years. Statz contacted every agency she could think of inquiring about Jean: had she used her Social Security number or tried to renew her pilot's license or get a passport? They even tried Interpol.

After a fairly exhaustive search, Statz concluded Jean was most likely dead.

The detective started talking with anyone involved with the case back in 1976. She found Linda, the only one of the Zapata children still living in Madison, working as a nurse at a local clinic.

"And we went into another room. And I explained who I was and that the investigation into her mother's disappearance was reopened," Statz remembers.

"And my gut dropped out. And I thought, 'Oh my god. Did you find her? I mean is she downtown right now? Is she out in the car?' You know, I thought they found her. They said no, but we're just going to reopen the case. The next question was…'Did my dad have anything to do with it?'" Linda remembers. "It just came out. And I said 'I don't know why I asked that.'"

Statz knew when she started investigating Jean's disappearance that Linda might have to face a horrifying possibility. "What's worse? My father killed my mother? Or my mother abandoned me," Statz asks.

Ever since Jean vanished when Linda was just 11, she not only believed she had been abandoned by her mother, she also believed she was to blame. "I overheard my brother and sister saying it was my fault she left because I was a brat. And I'm sure I was, 10, 11-years-old," she remembers.

Some 30 years later, Statz was convinced that Jean had been killed, but there was no body and no hard evidence. "It's one thing to believe something. It's another thing to solve something. And it's a completely different thing to charge it and be able to prove it in a court of law."

Early on in her investigation Statz went to the house where the Zapatas lived. There, she discovered a crawl space in the basement. It had not been mentioned in the original police reports in 1976. So Statz enlisted the help of some specially trained colleagues who can detect even the faintest scent of human remains.

Madison Police Officer Carren Corcoran has trained and handled cadaver dogs for the last ten years.

"It's hard to imagine that a dog can detect something from 30 years in a basement. How is that possible?" Schlesinger asks.

"I think that an entire body decomposing, possibly early on and in a space like the crawlspace, which was really [a] primo environment to contain scent. There's no wind. There's no rain. The temperature stays about the same all the time," Corcoran explains.

On Jan. 6, 2005, Statz, Corcoran and Cleo the cadaver dog went to work in the crawlspace. "Right away she started really working and working, and working the area of both outside the crawlspace, and into the crawlspace. And then she eventually provided a formal indication, which is a bark for Cleo," Corcoran remembers.

Then, a second dog reacted the same way. Police started excavating the crawlspace.

"We found some hairs. We collected bug carcasses and a Burger King cup. We found things. But we did not find anything that we could tie to Jeanette Zapata," Statz says.

Even though the search didn't turn up any useful evidence, Linda was pretty sure they were on the right track and looking at the right suspect: her own father. "I was hoping, hoping dearly that my dad would turn out to be innocent," she says.

Linda's brother and sister believe he didn't do it. But as painful as it might be, Linda was now determined to help the detectives find out whether that was true or not.

Helping the police would put Linda in an almost impossible position. In April 2005, word got back to her father, Eugene, that the case had been reopened. He was living with his second wife in Nevada, but he showed up suddenly and unexpectedly in Madison. Linda immediately called Detective Statz.

Statz says she was concerned Eugene might tamper with evidence, namely, Jean's remains.

Eugene managed to avoid the detective and flew back to Nevada. Two months later, Statz paid a surprise visit to his house, but it was clear that Eugene was not going to admit to anything.

The detective returned home without a confession, but not without hope: she had begun reconstructing his movements during that April visit to Wisconsin by pulling his cell phone and financial records. And that's how she found out he had rented a storage locker just outside Madison. She also discovered he had visited a landfill about 80 miles from that locker, but not before he had gone on a shopping trip to Wal-Mart.

"I call the Wal-Mart and I get faxed the receipt. And at that point, it became so very clear to me, you know, what he was actually doing," Statz says.

Here's what Eugene bought: two gallons of water, an odor absorbing mask, a few large containers, a tarp, two cans of Lysol, some Pledge wipes, scissors, recycling bags and paper towels.

Statz says it looked to her like supplies he would need if he was disposing of a body.

Statz looked into the history of the storage locker. Eugene rented it in 2001, just before he moved to Nevada, and had moved everything out of it on his last trip to Wisconsin in April 2005.

Statz says nobody had rented it since he had vacated it on April 14.

Officer Corcoran and the cadaver dogs were brought in again. This time they smelled something at the storage locker and in the car Zapata had rented. "I strongly believed that Jean's remains had been in the storage locker since 2001 when he rented it. And that on April 14th, when he moved out, that he took her to the landfill in the trunk of the car," Statz says.

Finding Jean's remains in the large landfill would be next to impossible. But the police were close enough to cracking this case that they thought maybe Eugene would finally confess, if not to them, then maybe to his daughter. They needed Linda's help again. And this time she'd have to make the most difficult decision of her life.

"A hundred times a day torn back and forth. How can I betray one or not betray the other? How could I do that to my dad? What kind of daughter am I? You know? But then my mom, she has no one else to speak for her," Linda explains.

Nine long months after the case was re-opened, there was still no sign of Jean, and still no evidence to tie her ex-husband Eugene to any crime.

It would take some new piece of evidence, something big, to make this case. And Det. Statz had an idea that would be, to say the least, one tough sell. "I asked Linda if she would place a phone call to her father and talk to him about her mother's disappearance," the detective says.

"I mean what kind of daughter is gonna betray their father? How could I do that? But then a second later it's like, how could I not do that for my mom?" Linda recalls.

In August 2005, almost 30 years after her mother went missing, Linda agreed to make two calls to her father, and let the police tape everything. In the recorded call to her father Linda asks, "Just between you and me, can you at least tell me if - do you think she's alive?"

"Well, first of all. I didn't have anything to do with her disappearance or anything - but after all these years, you gotta think that no, she's not," Eugene replied.

It took a while, but Linda worked herself up to making an awkward, and painful accusation. "I don't know. I guess my gut is that you did it. Which…," she said.

"Wow, that's pretty powerful," her father replied.

"I know it is, but I still love you and nothing's changed between me and you," Linda said.

The phone calls helped, but Statz needed more. So she went back to Nevada, where Eugene was living, this time armed with a search warrant, which led to a safety deposit box and a discovery that would change everything.

"We found three envelopes marked, 'Destroy. Do not read,'" And despite the instructions, Statz explains, "We couldn't read 'em quickly enough. What they included were details of Eugene following, and in my opinion the word stalking could be used, Jeanette from the time that she filed for divorce - May 12th, 1976, up until about the beginning of September of '76."

Eugene's detailed notes were the evidence prosecutor Bob Kaiser had been hoping for. In a written statement sent to 48 Hours, Eugene says he was just building a case to help him win custody of his children.

But Kaiser believes the notes show Eugene's obsessive state of mind when his wife filed for divorce. "Was he going into her pants and sniffing the crotch of her pants to see if it smelled like spermicidal jelly? Yes. That's what he was doing. Breaking into her house, looking through everything in the house," Kaiser says.

But it's hard to prove a murder case in front of a jury without a body, so police were hoping their cadaver dogs would find Jean's remains in that huge landfill Eugene had visited on his last trip to Wisconsin. They looked for five days and turned up nothing.

So Kaiser went with what he did have - circumstantial evidence that Jean was murdered. And 30 years after the case began, Kaiser ordered police to arrest Eugene Zapata.

Linda's father was charged with killing her mother, and on Sept. 4, 2007, Eugene went on trial for first-degree murder.

Once again Linda would play a major role in the case against her father. She became the first witness for the prosecution. Asked what was going through her mind as she was on the witness stand, Linda says, "Mainly, although I never regret for a second doing it, I felt bad."

The judge ruled testimony about what the dogs found was unreliable and threw it out. So prosecutors had to rely on evidence of Eugene's movements, and those notes he tried so hard to conceal.

Eugene's one big mistake, argues the prosecution, was answering the phone on the morning of Oct. 11, 1976, a morning he was barred by court order from being at the house.

It takes the defense less than one hour to present their case. They argued that the prosecution failed to connect Eugene to any crime.

"But you will not leave with proof, and certainly not proof beyond a reasonable doubt. I ask you to find Eugene Zapata not guilty," defense attorney Steve Hurley said in closing arguments.

Eugene never talked in court, and never talked to 48 Hours.

"We had come so far from nothing. We were asking a lot of a jury to convict without a body and convict without DNA," Statz says.

But anyone looking for answers to this 30 year-old mystery would have to keep looking. Because behind closed doors, the jurors argued and debated, but even after four days they could not decide what happened to Jean, no matter how hard they tried. They left the judge no choice: he declared a hung jury.

On Sept. 17, 2007, Eugene walked out of court a free man. But the father of three who kept silent during his trial was about to stun everyone.

After three decades, two investigations and one trial, Eugene is about to break his silence and tell a chilling story.

"I felt he had gotten away with it for 30 years. But I don't like a guy to get away with a crime for 30 minutes," Kaiser says.

The prosecutor was ready to go back to court to try Eugene again. And that's when Eugene suddenly announced he was willing to plead guilty.

Eugene was ready to finally answer the 30-year-old question: what happened to his wife? But he'd only give that answer if prosecutors would reduce the charge from murder to reckless homicide.

The district attorney thought that Eugene's daughter Linda should be the one to decide whether they should accept his plea, or start all over again in court. "I said, 'The only thing I want is for him to admit he did it. Tell us what happened to her. How he did it. And above all, I needed to see it come out of his mouth.' I needed to see him say, 'I killed her,'" Linda says.

The deal was done. Eugene, who had lied to all his children, broke his silence, and told his story to Statz.

Eugene told Statz that he had gone over to the house, and that shortly thereafter, an argument broke out. It turned violent in the kitchen, he said, when he grabbed a paperweight and hit Jean in the back of the head.

Statz says Jean lay on the ground still alive; the detective says Eugene then strangled her. "He told me that he didn't have an actual memory of his hands on her throat. But he had a memory of his hands and his forearms hurting a lot. He got a cord, like a tent cord, and wrapped that around her neck to make sure that she was dead."

According to Eugene's statement, he cleaned up the kitchen and began a grisly 30 year odyssey with Jean's body, burying it, exhuming it, and re-burying it. He claims his wife was never in the crawlspace. He says for 25 years, she was buried in a vacant lot he bought right after the murder. Then he says he moved her to the storage locker, where she stayed until April 2005, when Eugene heard the case had been reopened. Then he says he came back here, cut her body into pieces and took her to the landfill.

Linda asked that her father's entire confession be videotaped. The defense agreed, on the condition that she would be the only person to see it, and then it would be locked away forever.

Asked what it was like seeing that confession, Linda says, "I just still felt sick to my stomach. I felt so sad. But it was also very therapeutic. I felt like I was there for my mom again. The truth is comin' out. This is what happened. And it was big, almost a relief."

Eugene Zapata returned to court once more, this time to face his sentence and to face his daughter. Linda directly speaks to her father," Dad, although I don't condone what you did to mom, I do forgive you and I love you."

Zapata said nothing. He was sentenced to five years for reckless homicide - all the judge could give him. And under the sentencing laws of 1976, when the crime was committed, Eugene will have to be released after only three years in prison.

Kaiser says justice was done. "Because we know what happened. In this case, on these facts, that was justice."

In that written statement he sent to sent 48 Hours, Eugene says the real reason he took the plea was to avoid the expense and embarrassment of a second trial. In fact, in spite of his plea his wife and two other children continue to believe he's innocent. But Linda however believes the truth is finally out.

"I have a huge weight off my shoulders. Huge," she says. "You know it's such a corny line but the truth, you know, the truth will set you free. It's true. At least for me."

Linda now knows her mother didn't abandon her and she could begin mourning. On April 12 2008, she held a memorial service in the same church where Jean had once been a member.

The police and prosecutor who worked so hard to make sure Jean was not forgotten, also gathered to honor the memory of a woman they never knew.

"You know, there's sadness, but I just had a smile on my face a lot of the time during the service, 'cause she deserved this. I think she's up there just saying, you know, "What took you guys so long? Okay, finally we got this." And.-- just knowing that she's at peace now," Linda says.

Linda has been cut off from her immediate family. Her father, brother and sister no longer speak to her.