In 2005, investigators called Eugene, who had remarried and moved to Nevada in 1997, and questioned him. The following day, Eugene cleared out a storage locker which he had rented in 2001. Police searched the locker with cadaver dogs a short time later. The dogs again detected the scent of human remains, and they also indicated the presence of human remains in the attic and crawl space of the Zapata residence, and in a vehicle Eugene rented during a visit to Wisconsin in 2004. During his trip to Wisconsin, he purchased trash bags, some large containers and cleaning supplies and visited the Juneau County Solid Waste Landfill; records indicate he dropped off items weighing 60 pounds. A search of the landfill turned up no clues, but the cadaver dogs again indicated the odor of human decomposition.
In August 2006, Eugene was charged with first-degree murder in connection with Jeanette's presumed death. He was tried for her murder in September 2007. The jury deliberated for 30 hours, but was unable to reach a verdict, and a mistrial was declared. In February 2008, Eugene made a plea arrangement with prosecutors. He pleaded guilty to reckless homicide in Jeanette's death and admitted he had "snapped" during an argument about their divorce. He stated he hit her on the head with a paperweight and he strangled her to death, then dumped her body in a rural area east of Madison. Eugene explained that later he had purchased land in Juneau County, Wisconsin, moved Jeanette's remains there, and buried them. The body stayed there until 2001, when Eugene moved to Nevada. He placed the body in his storage locker at that time, only retrieving it when the police questioned him in 2005. Then he dismembered Jeanette's body, wrapped the pieces in plastic bags and put them in a dumpster at the Juneau County Landfill.
Eugene was sentenced to the maximum of five years in prison for reckless homicide. He had to be sentenced according to the laws in 1976. With time off for good behavior, he could be freed in as little as three years and one month. He also agreed to pay his daughter Linda $5,000 in restitution for the expenses related to Jeanette's death. In spite of his confession, Eugene later stated he only pleaded guilty to avoid a second trial. His second wife and two of his three children with Jeanette still believe he is innocent. Linda, who was ten years old in 1976 and came to believe her father is guilty, is no longer on speaking terms with the rest of the family.