Attorney Howard Kurtz said detectives zeroed in on Brad Cooper and didn't look at other possible suspects.
"The Cary police department concluded that Brad Cooper killed his wife before they even began the investigation," said Kurtz in his opening statement.
Kurtz called the investigation "inept" and said police ignored evidence in their zeal to pin the murder of Nancy Cooper on her husband. He told jurors evidence will show she was alive the day she was reported missing, but police concluded she was killed earlier.
Kurtz admitted to the jury that Brad Cooper cheated on his wife, but said he regretted it. He also said Nancy Cooper had a relationship outside the marriage and that the couple was in the process of getting a divorce.
Prosecutors wrapped up their initial presentation late Wednesday, saying Brad Cooper killed Nancy Cooper in anger over her intention to leave him and take the children.
In her opening statement Wednesday, prosecutor Amy Fitzhugh told jurors that Cooper made statements to police that were untrue and refused to cooperate before Nancy Cooper's body was found.
Cooper told police his wife went for a jog on the morning of July 12, 2008, and never returned. A two-day search found Nancy Cooper's body not far from the couple's home.
The Coopers relocated to Cary from Canada in 2001 when Brad Cooper took a job at Cisco Systems in Morrisville. He studied computer science at the University of Calgary and took graduate business courses at North Carolina State University.
Evidence in the case against Cooper was scheduled to begin Monday, but jury selection took longer than expected.
The massive search for Nancy Cooper made national news. A few days after first being reported missing, she was found strangled near a drainage ditch in a neighborhood under construction not far from the couple's Cary home.
Brad Cooper was arrested three months after the murder of his wife. He has spent every day since then in the Wake County Jail - except for last week when he spent each day in the courtroom.
The document said Cooper told investigators he received a call from Nancy on the day she disappeared. Cell phone records indicated that he did receive a call from their home phone.
Investigators, however, suggest in the search warrant that Cooper might have been able to make the call himself due to his knowledge of Voice over Internet Protocol from his job as an engineer for Cisco Systems. He also had the ability to connect to the internet on his cell phone.
Friends of Nancy Cooper's have said Brad Cooper was extremely controlling.
Kurtz said in his opening statement that part of the reason for that was that Nancy was too free with money and Brad had to put her on a strict cash budget.
He also said Cooper took his wife and children's passports because he was afraid she'd leave the country with his children.
Nancy Cooper's parents now have custody of the couple's two children in Canada.