A 58-year-old businessman and founder of an Adams County software company was arrested Friday on murder charges in a bizarre office shooting at the end of the year that left him injured and another man dead.

Adams County District Attorney Don Quick filed charges against William Rex Fowler in the shooting death of 42-year-old Thomas Ciancio, his former business partner at Fowler Software Design.

Investigators say Fowler shot Ciancio three times in the head with a 9mm Glock handgun when Ciancio came to Fowler Software Design to collect $9,900 in severance pay.

Police had originally thought Ciancio was the gunman but later described him as a victim.

Ciancio, who was Fowler Software’s chief operating officer, resigned Nov. 23 in a dispute over the way the company was being managed.

On Dec. 29, Ciancio agreed to a settlement and to sign a waiver of release in exchange for the payment, company chief executive Laura Zaspel told investigators, according to a court document supporting the filing of charges.

Employees of the software company told investigators Ciancio had blamed Fowler for the company’s recent financial difficulties.

The employees said Fowler had taken about $200,000 of the company’s money without asking and gave it to a church or charity, according to the arrest affidavit.

Ciancio had “become very frustrated with William Fowler,” according to the arrest affidavit.

Ciancio arrived at 10 a.m. Dec. 30 to collect his check. He chatted with employees, asked about their holidays and was preparing to attend his son’s birthday party later that day.

Ciancio asked to speak to Ubaldo Ciminieri, the company’s vice president of sales and marketing, but he had stepped away from his desk. Ciancio then went to Fowler’s office.

Two minutes later, according to the affidavit, employees heard gunshots. Police were called by another tenant in the Elati Building, near West 84th Avenue and Elati Street in unincorporated Adams County.

When deputies arrived, they saw Fowler making his way through the front door, bleeding from the head. Investigators said he took one step past the threshold, then went back in. Police rushed into the building, escorted Fowler back out and called for an ambulance.

When Fowler tried to speak to deputies, blood poured from his mouth. They asked if Ciancio was still in the building, and he shook his head up and down to say “yes.” They asked if Ciancio shot him and Fowler did not respond, investigators said.

Fowler was taken to Denver Health Medical Center, where he underwent surgery for a wound from the bottom of his chin through the top of his head. During the surgery, police said, Fowler’s hands were bagged to protect evidence of gunshot residue, which was later collected by investigators.

Inside Fowler’s office, police found Ciancio’s body. They said he appeared to have been sitting at a table when he was shot. They also found what they believe is the murder weapon and four 9mm Luger shell casings. They found a handgun magazine on the table and another in a closet in the office.

Investigators say the gun was registered to Alexander Hyung Fowler, 26, who lived at 1413 L. Ron Hubbard Way in Los Angeles when it was purchased. In interviews with police, Alexander Fowler said he gave the gun to his father for Christmas in 2007.

Police also found a briefcase and a typed note, dated Dec. 30 and signed by Fowler. The note said nothing confidential was in the satchel and that it should be given to his wife, Janet.

When Janet Fowler was interviewed by detectives, she demanded the briefcase.

“It is important to me and my church. It is religious material and I want it now,” she said to investigators. “Even if you looked at it, and read it, you would not understand anything in it. Because it is way above a normal person and you would not know what it meant. I want it back right now.”

Janet Fowler also reportedly told investigators that her husband “is a Scientologist and would not have gone without a fight. He would have grabbed a gun in a struggle and would not have let someone shoot him.”

She also told investigators that Ciancio had sent e-mails to Rex Fowler, threatening to hire an attorney and sue over money he said was owed him.

Adams County officials said Fowler is in custody but would not say where he is being held. He was last known to be at Denver Health Medical Center, but his name no longer appears on patient rosters.

No court date has been set for Fowler.

Ciancio’s family members said they did not want to comment on the case. Calls to Fowler’s Broomfield home and to the Church of Scientology were not returned Friday.

Several websites that scrutinize Scientology have been following this case, with links to records that allegedly reveal Fowler was a senior Scientologist. The sites claim that Fowler Software was a member of the World Institute of Scientology Enterprises.

According to the arrest affidavit, Ciancio’s brother gave investigators four binders of Scientology materials that Fowler had given to Ciancio, asking him to study the religion.

Ciancio was raised a Roman Catholic, his family said, and had attended New Hope Presbyterian Church in Castle Rock.

Jeremy P. Meyer: 303-954-1367 or jpmeyer@denverpost.com

This article has been corrected in this online archive. Originally, due to an editing error, the son of Rex Fowler was misidentified. He is Alexander Hyung Fowler.