The 36-year-old flight instructor - who was divorcing her husband - was never heard from again.
According to a search warrant executed by police in August but kept sealed until Thursday morning, dogs trained to detect human remains reacted to two locations connected to Eugene Zapata - a crawl space in the couple's former home and a storage locker in Sun Prairie.
Two days after Jeanette Zapata's children saw her for the last time, Ivan Norton, an accountant at Frickleton School of Aeronautics, reported her missing because she hadn't come to work.
"If she told you to make an appointment at a certain time, she was there ahead of schedule to make sure it all went right," Norton, 69, said Thursday. "She was very nice and very prompt and that was the whole thing that was concerning us. She was like a time clock."
Immediately after she disappeared, her purse and other belongings, including her new car, were found at the home, but a .30-06 rifle was missing.
Investigators said in the search warrant:
Officers have questioned Eugene Zapata several times over the past 30 years and he sometimes provided contradictory statements.
Zapata told police he argued with his wife over visitation rights to their children a few days before she disappeared. The day she vanished, they met with the La Follette High School principal to discuss their oldest daughter. One time he told police he called the morning of Oct. 11 to cancel the meeting. On another occasion, he said he went to the house at 9 a.m. to pick her up.
Jean Zapata had obtained a court order that restricted his time with the children in the home to two hours on Saturday mornings.
His employment records at the state Department of Transportation indicate he worked from 7:45 to 8:45 a.m. the day she disappeared, was off work the following day, Oct. 12, and then came in to work at 12:30 p.m. Oct. 13.
He told police he took Oct. 12 off to care for his children at home, but investigators verified the children were at school.
Zapata did not respond to messages from the State Journal asking for an interview. In a 1987 State Journal article, he said he believed his former wife ran away.
"It may have been just the pressure of it because I filed for custody of the kids," Zapata said then. "She was a very strong-willed person. If she made up her mind that she wanted to disappear, she could do it."
Investigators suspected Zapata, but lacking leads they had shelved the case.
It was reactivated a year ago after one of Jean Zapata's childhood friends called asking about its status, Snyder said.
New detection techniques, including "cadaver dogs" that can find faint odors of human remains, pushed the investigation forward.
According to court documents, dogs twice signaled that they had found the scent of human remains in an unused basement crawl space at the Zapatas' former home on Indian Trace, and a human hair was excavated. Police will not say whether test results indicate that it belonged to Jean Zapata.
Eugene Zapata sold the house in 1997. In 2001, he moved to Nevada. He rented a storage facility in Sun Prairie that year and listed its contents as "boxes, mixture of son's and parent's stuff."
According to the search warrant:
On April 13, 2005, police left a message for Eugene Zapata with his wife in Nevada. The next day, the locker's key was returned to U-Store Mini Storage in Sun Prairie. The empty locker remained locked until Aug. 10 and 11 when police opened it.
Dogs detected the scent of decomposing or decomposed human remains inside and around the locker, the search warrant indicates. That prompted a search of four acres in rural Juneau County owned by Zapata since 1978.
Eugene Zapata was arrested for allegedly murdering his wife Jean Zapata, who disappeared from their East Side Madison home 30 years ago.
The investigation into what happened Jean Zapata was dormant for years. The 36-year-old Madison woman and mother of three disappeared in 1976, but the case only returned to the spotlight in December 2004.
Here is a timeline in the investigation:
December 2004: Cadaver Dogs Search Former Home
Two cadaver dogs searching the basement of Jean Zapata's former home and indicated hits of human remains. A human hair was taken from the site, police said.
August 2005: Cadaver Dogs Search Storage Locker
Two cadaver dogs separately indicated hits of decomposing human remains at a Sun Prairie storage locker that Eugene Zapata had rented.
August 2005: Cadaver Dogs Search Juneau County Lot
Police also used cadaver dogs to search a 4-acre lot owned by Eugene Zapata in Juneau County.
December 2005: Police Call Case "Foul Play"
Madison police officially called the case "foul play" and named Eugene Zapata their one and only suspect.
February 2006: Eugene Zapata Denies Connection To Wife's Disappearance
In a telephone interview with WISC-TV from Henderson, Nev., Eugene Zapata denied any connection to his wife's disappearance.
March 2006: Police Search Juneau County Landfill
Madison police conducted a week-long search of the Juneau County land-fill near Mauston. They said that they are searching for Jean Zapata's remains and containers that they believe belonged to Eugene Zapata.
August 2006: Eugene Zapata Arrested For Murder
A second trial seemed less likely after reports surfaced earlier this month that a plea deal had been struck.
As part of the agreement with prosecutors, Zapata had to tell authorities how he killed his wife and where her body was hidden, WISC-TV reported.
During Monday's proceedings, Dane County chief prosecutor Bob Kaiser asked the court to accept an amended charge of homicide by reckless conduct. Kaiser earlier told the court that the deal with Zapata includes a statement to police about why Zapata went to her house, how and why he killed her and what he did with her.
Kaiser said that Zapata confessed to police and that he believes Zapata's statement will be truthful and complete.
Prosecutors said that Zapata told police that he went to his wife's house in 1976, had an argument and "snapped." He told them that he grabbed a metal draftman's tool and hit her in the head multiple times. He said that she then dropped to ground and he strangled her. He apparently told investigators that he "strangled Jeanette Zapata manually until his hands hurt." He also wrapped a cord around her neck.
Zapata said that he wrapped her body in a tent and drove it to an area near Highway 151 and Reiner Road, where he hid it in some underbrush. He transferred her remains a short time later to some Juneau County land that he owed. There, he buried her body -- which remained there for 24 years -- before moving her remains to a Sun Prairie storage locker, where it was eventually cut into pieces and later disposed of at a Mauston landfill. He moved the body from the Juneau County because he planned to sell the land. Blanchard said because Jeanette Zapata's body was dumped in numerous Dumpsters at the landfill, there is no way to recover her remains.
Linda Zapata, the youngest of Eugene and Jeanette Zapata's three children, gave a statement in court. She said that she was torn over testifying against her father earlier, but she's glad that he agreed to the plea deal. She said his confession is "a gift."
"By confessing to Mom's murder, you have given me and others a precious gift, a chance to grieve, mourn and heal," she said. "Mom deserved no less than that Mom deserved the truth about what really happened that morning, and I thank you for finally giving her that."
She added that she still loves her father and forgives him, although she doesn't condone what he did.
Kaiser said that he thinks the agreement is the best possible option for "truth and justice." Likewise, Blanchard called the resolution to this case a huge achievement for justice.