On October 31, 2005, photographer Teresa Halbach was scheduled to meet with Steven Avery at his home on the grounds of Avery's Auto Salvage to photograph his sister's minivan for a sales ad in Auto Trader Magazine. She went missing the same day.

On November 11, Avery was charged with the murder of Halbach after her car and charred bone fragments were found at the salvage yard. He maintained that authorities were attempting to frame him for Halbach's disappearance, to make it harder for him to win his pending civil case regarding the false sexual assault conviction. To avoid a conflict of interest, Mark R. Rohrer, the Manitowoc County district attorney, requested that authorities from neighboring Calumet County lead the investigation. Manitowoc County Sheriff's Department officials remained involved in the case, however, participating in searches of Avery's trailer, garage and property, leading to accusations of tampering with evidence.

On March 2, 2006, Avery's nephew, Brendan Dassey, was charged with being a party to first-degree intentional homicide, mutilation of a corpse, and first-degree sexual assault after confessing to investigators; he was later convicted in a separate trial. Dassey's attorneys have filed a writ of habeus corpus in the district court for his release or retrial, claiming constitutional rights violations due to ineffective assistance of counsel and an involuntary confession.



Ken Kratz, the district attorney of Calumet County, was assigned as special prosecutor in the case, and Manitowoc County Circuit Court Judge Patrick Willis presided over the trial.

On March 18, 2007, Avery was found guilty of murdering Halbach, not guilty of mutilating a corpse, and guilty of illegally possessing a firearm. On June 1, 2007, he was sentenced to life in prison without the possibility of parole for the murder of Halbach. He was also sentenced to five years for felony possession of a firearm, to run concurrently with the murder sentence. Initially housed at the Wisconsin Secure Program Facility in Boscobel, he was moved in 2012 to the Waupun Correctional Institution in Waupun.

In January 2016, People reported on the makeup of the trial's jury, revealing that one of the jurors in Avery's trial was the father of a Manitowoc County Sheriff's deputy, and another juror's wife was a Manitowoc County clerk. Juror Richard Mahler, who was excused from the trial after the jury had begun deliberations due to a family emergency, later commented on the trial and verdict. He stated that, in an early vote, seven of the jurors voted not guilty, and he was mystified as to how the jury eventually agreed on a guilty verdict. Another juror told the filmmakers of Making a Murderer that they felt intimidated into returning a guilty verdict, as they feared for their safety.