SAN JOSE — A mentally ill inmate who died at the Santa Clara County Main Jail in September, a week after being forcibly removed from his cell by guards who shot him with plastic projectiles from a riot gun and doused him with pepper spray, did not die from his injuries, according to an autopsy report.

Walter Roches, 32, of San Jose, died of natural causes from sepsis — a severe blood infection that can lead to organ failure — from a chronic urinary tract illness, complicated by “exhaustive mania” after he refused to take medication he had been prescribed for schizophrenia and bipolar disorder, according to the report from Santa Clara County Medical Examiner Michelle Jorden.

High blood pressure and a history of stimulant drug use also contributed to his death, Dr. Jorden concluded.

Roches was found dead in his cell on the fourth floor of the main jail in San Jose on Sept. 28, one week after guards extracted him from a cell after he refused to leave to go to the psychiatric ward.

The death is one of several controversies in recent months involving the jail, its guards and Santa Clara County Sheriff Laurie Smith.

In August, inmate Michael Tyree, who was behind bars for a probation violation on a minor drug charge, died in custody at the jail after allegedly being beaten by guards. Three correctional deputies — Jereh Lubrin, Rafael Rodriguez and Matthew Farris — have been charged with murder in his death.

Following Roches’ death, the sheriff in November banned jail guards and medical staff from using plastic bullets to subdue inmates, a practice that critics have said is excessive. She also prohibited the use of chemical sprays in situations involving mentally ill or developmentally disabled inmates, unless the inmate has made an overt attempt to harm himself or others. And her directive required jail guards to call a mental health professional to the scene to speak such inmates in all planned cell extractions or planned uses of force.

“We mourn the loss of Mr. Roches, who died of natural causes,” said Sgt. James Jensen, a spokesman for the Santa Clara County Sheriff’s Office. “The medical examiner’s report is clear that the removal of Mr. Roches from his cell, a week prior to his passing, did not cause his death.”

The autopsy found that Roches had been arrested Sept. 5 after “a physical and sexual altercation” at Evans Lane Wellness and Recovery Center, a mental health facility where he lived that is located about a mile east of Willow Glen High School. He was taken to San Jose’s Valley Medical Center, where authorities said he assaulted a member of the medical staff.

He was released from custody and rearrested on Sept. 20 by Milpitas police and booked into jail on suspicion of two additional counts of assault and battery, being drunk in public and a traffic-violation warrant. The next day, he appeared disheveled and refused to talk or come out of his cell, the report said.

“Mr. Roches repeatedly refused his medication (Zyprexa) while in the main jail so his mental illness was left untreated,” the report said.

Roches sustained numerous large bruises all over his body, and injury to two areas that bled under his scalp after he was forcibly removed from his cell, the report found. However, his head trauma during the cell extraction “did not cause Mr. Roches’ death, but the use of force may have heightened and accelerated an already delirious state.”

However, LaDoris Cordell, a former judge who is chairwoman of the county’s blue-ribbon commission probing jail issues, said she was “very troubled” by Roches’ head injuries.

“Given that Mr. Roches’ death was attributed to sepsis, one must assume that he was extremely weak and in excruciating pain and hardly in a position to resist unless he was flailing in pain,” she said. “Why, then, was there bruising all over his body? This autopsy report raises many more questions than it does provide answers.”