Amidst all the murders in San Francisco, some suspicious deaths are hidden in a secret burial ground of bureaucracy.

Sometime past midnight on Labor Day of last year, 22-year-old John "Daniel" Schirra was running nude along an Ingleside District street, yelling for help. He was in the grips of a bad acid trip, and had either just been stabbed or was about to be. He tried to stop two cars and rang a random doorbell at one of the neighborhood's modest homes. Someone called the police to report that a naked young man, who may have been bloody, was running in the street. No one stopped to help.

Around 3:15 a.m., Schirra, a San Francisco State University student, was found dead. His body was in the fetal position under a juniper tree on a sloping, garbage-strewn lot off the 2600 block of San Jose Avenue. The resident who discovered Schirra's body says it appeared to have numerous stab wounds to the torso.

Police began a homicide investigation, speaking to people who saw Schirra that night and interviewing his friends. For a short time, they even had a suspect. But when the investigation did not pan out, police began to treat the case as an undetermined death. They told Schirra's parents their son probably stabbed himself and that he may have died from an accidental head injury. But more than a year later, there are no autopsy or police reports available to support that theory.

Paul Trapani
The vacant lot off San Jose Avenue where the nude body of John “Daniel” Schirra was found in the fetal position.
Photo courtesy of the Schirra family
The vacant lot off San Jose Avenue where the nude body of John “Daniel” Schirra was found in the fetal position.
John “Daniel” Schirra
Photo courtesy of the Schirra family
John “Daniel” Schirra
Hugues de la Plaza.
Hugues de la Plaza.
Robert Peplies when he graduated.
Courtesy of Barbara Peplies
Robert Peplies when he graduated.
26 Sargent Street, where the brutally stabbed bodies of Robert Peplies and Linda Almanza were found.
26 Sargent Street, where the brutally stabbed bodies of Robert Peplies and Linda Almanza were found.
Robert Peplies’ sister, Barbara Peplies.
Sheena Patrick
Robert Peplies’ sister, Barbara Peplies.

The unusual circumstances of Schirra's death gave him entrée to an exclusive fraternity of four San Francisco residents whose deaths in 2007 appear to be self-stabbing. Adding to the perplexing nature of the deaths, information about three of the cases has fallen into a bureaucratic black hole between the homicide detail and the medical examiner's office. Criminal and medical experts say it's highly unusual that the autopsy and police reports are still not available for three of the cases, two of which occurred more than a year ago.

The most notable of the four deaths is that of French national Hugues de la Plaza, who was found dead in his Hayes Valley apartment on June 2, 2007. His case garnered international attention when police called his death a suicide even though no note or bloody knife was found inside the apartment. Then there are Robert Peplies, 45, who died of knife wounds to the torso on August 31; and Jeremy Hill, 34, who was found dead in his bedroom on December 8. Hill had cuts to his arms and had bled out into a bowl. While Hill's death had the earmarks of suicide, the medical examiner kicked the case back upstairs to the homicide detail for further investigation four months later.

The medical examiner typically classifies suspicious deaths after reviewing the autopsy, toxicology reports, DNA analysis, and police reports. But that has happened only in de la Plaza's case. Some family members of the victims say they have grown weary of seeking answers from the endless circle of secrecy that surrounds the cases. Meanwhile, the San Francisco police won't discuss a case until the medical examiner completes the autopsy report, the medical examiner refuses to say why the report is taking so long, and police crime lab officials say nothing at all.

And it's not just the victims' families who are raising questions. A federal court embarrassed the San Francisco Police Department when it ordered all of the de la Plaza forensic evidence be turned over to the French police, who have taken the investigation back to Paris.

Some family members suspect the delays are a result of either colossal incompetence or a conspiracy to falsely reduce the city's annual homicide numbers, which last year threatened to exceed the politically radioactive number of 100 (2007 was a mayoral election year, and the official homicide count was 98). One homicide lieutenant strongly denies such speculation, and SF Weekly found no evidence of such manipulation.

Supervisor Ross Mirkarimi says the problem of delayed death classifications is just another symptom of a broken justice system that produces too few convictions for violent crimes, alongside an underperforming police department that has operated without accountability for years. Mirkarimi, who chairs the Public Safety Committee, says he has heard anecdotally that there are between 10 and 20 unclassified deaths from 2007, which could alter homicide statistics by as much as 20 percent. He says the committee has requested the exact numbers from the police department, to no avail.

But Mirkarimi says it is unfair to lay the problems entirely at the feet of the police department. The problem, he says, reaches into the offices of Mayor Gavin Newsom and Police Chief Heather Fong.

Schirra never spoke of suicide or hurting himself, says Tim Sandberg, who had known Schirra since the two grew up together in the Southern California town of Walnut.

Schirra was doing well in the broadcast and communication arts department at San Francisco State. He was looking forward to graduating, and wanted to begin recording musicians. According to Sandberg, Schirra had supportive parents and a tight-knit circle of good friends who loosely revolved around a band called the Fucking Buckaroos, which Sandberg plays in.

A year later, Schirra's friends still wonder how his death could have been an accident. The idea that he stabbed himself has been particularly hard to accept. "There's so many loose ends in this case," Sandberg says. "People have so many different opinions about what happened, and nobody is sure."

Statistically, they have reason to be skeptical. Self-inflicted stabbing deaths are rare. In 2005, the most recent year for which national statistics are available, 32,637 people committed suicide in the United States. Only 590 did so by cutting or piercing, and of those deaths, most were slashing or cutting to the wrists and, to a lesser degree, the throat, according to Lanny Berman, the director of the American Association of Suicidology. "Suicide by stabbing is very rare, and it's particularly rare for someone to stab themselves in the torso," he says.

Amy Hart, chief of the San Francisco Medical Examiner's Office, refused to comment for this story about the frequency of self-stabbing suicides, but last year she told de la Plaza's family she had seen only two such cases in her 30 years as a forensic pathologist, and in both cases the victims had a history of psychosis, according to de la Plaza's ex-girlfriend, Melissa Nix, who attended the meeting. (Of the four cases, only Robert Peplies had shown some signs of mental illness, though he had never been officially diagnosed.)

The night he died, Schirra had been at a barbecue. At some point he took his first-ever tab of LSD, according to friends, and began to have a bad trip. Around 11 p.m., he returned to the Oceanview house he shared with several roommates. One friend, Ricky Pugh, was worried about Schirra's state of mind and tried to stay with him. Schirra said he wanted to be alone; he abruptly left on foot in the direction of the Ingleside District. Pugh started to follow, but gave up when it looked like Schirra was heading to a girlfriend's apartment.

In the last few years, the Ingleside has experienced a rise in gang activity and violence. In fact, there had been four murders during the previous four months in the neighborhood.

There is no reliable information about what happened between the time Pugh stopped following Schirra and when Schirra's body was found. The anecdotal information, which is spotty, comes thirdhand from Schirra's friends, who got it from his parents, who got it from police in April.

Police found Schirra's clothes piled up by a bench at Ocean View Park. They told his parents they think he stabbed or cut himself several times, possibly once or more in the throat. The wounds were not life-threatening, but Schirra may have panicked at the sight of blood and tried to get help from two passing motorists and at one residence. At some point, police think he fell on a set of stairs and fatally struck his head. But the police won't say where those stairs are. After the fall, Schirra supposedly made his way to the grassy lot, where he collapsed and died.

Lieutenant Michael Stasko, who took over command of the homicide detail in March, verified some aspects of the theory and added that homicide inspectors spoke to witnesses who saw Schirra that night and claim he did not say he was being chased or threatened.

Lead investigator Kevin Jones could be right with the accident theory, though it is publicly unknown what facts he's using to support it, since the police report is not out yet. Schirra's parents, John and Robin Schirra, find no fault with Jones' work. "The police department was extremely generous with what they found," says John, an engineer who lives in Walnut. "They walked us on the route he took that night and took us to the lot and explained how they found him. We're satisfied."

But the lack of autopsy and police reports, fingerprints, or DNA analysis on a knife that was found have created doubt among some of Schirra's friends. There may be similar doubt among police ranks. Someone in the homicide detail reported his death as a murder by blunt force in its annual report to the California Department of Justice. The state finalized those statistics last month. Stasko says he has been so busy since he took over that he hasn't reviewed the 2007 list and didn't know Schirra's name was on it.

There are also lingering questions about the thoroughness of the homicide investigation. There is an overarching principle in criminal investigation that when there are two or more theories about a particular crime, the investigating agency should pursue them all to their logical conclusions, says David Klinger, dean of the graduate program in criminology at the University of Missouri. So unless police were able to determine for certain that Schirra stabbed himself and then accidentally struck his head, the principle would dictate that they should have continued an aggressive homicide investigation.

Stasko says it is policy to investigate multiple theories if there is not enough evidence to prove one theory over another. "We always investigate anything that could be a homicide," he says. "While we're waiting for the cause of death to be determined, it's full speed ahead." But homicide investigators did not interview residents who live near the lot where Schirra's body was found. "They didn't talk to me or anybody who lives in my building," says Samson Williams, who lives immediately adjacent to the lot. "I didn't see or hear anything, but I have to say it kind of surprised me."

Jim Avery, who lives across the street from where Schirra was found, says police did not speak to him either. He says there was an active crack house operating across the street from the lot. Avery says he was attacked for no apparent reason one night. "Some guy punched me to the ground, kicked me a few times, and then ran into the crack house," he says. "There were a lot of problems there. I filed a police report but they never found the guy."

On August 31, 2007, Javier Almanza stopped by the Ingleside Heights home he owns at 26 Sargent Street and found a bloody scene. The body of his ex-wife's friend Robert Peplies, 45, was crumpled in a closed-in porch area near the entrance. Peplies had been stabbed several times in the torso. When police arrived, they found another gruesome scene in the upstairs bedroom. The stabbed and bludgeoned body of Almanza's ex-wife, Linda Almanza, 37, who lived in the house, was at the foot of the bed with gaping wounds in her throat and chest. A bloody metal pipe was near her body, and more than one bloodied knife was found in the residence, according to her autopsy report, which was released in January.

Police are not discussing the Sargent Street case more than a year after the deaths. But the Peplies family is. According to Robert's sister, Barbara Peplies, who lives in Tennessee, the San Francisco homicide detail has performed a very limited investigation. Initially police looked closely at Javier Almanza as a suspect, but once he was ruled out, they began to call the deaths a murder/suicide. The current theory is that Peplies first killed Linda Almanza in the bedroom, and then went downstairs and stabbed himself.

The Peplies family doubts that Robert, whom they called Bert, could be responsible for such a brutal murder, especially since he and Linda had been close friends for 17 years. But they admit it may be in the realm of possibility. Robert had a degree in philosophy, but in later years he developed a heroin addiction. Barbara Peplies says her brother had also begun to exhibit signs of mental illness, though he was never diagnosed. "My brother was a drug addict and he was on a lot of medications," she says, "but Bert was never the type of person who would hurt himself or hurt someone else. And he was so squeamish, I can't imagine him murdering someone and then committing suicide like that."

From the little that is known about the case, there could be a third party involved. Crime scene technicians found blood outside the house, and one neighbor told a reporter that two casually dressed men were seen walking up the stairs to the home the day before the bodies were discovered.

The Peplieses say they became concerned when lead homicide inspector Karen Lynch chose not to interview any of Robert Peplies' friends or the person with whom he shared a small apartment near City Hall. Lynch also declined to read a journal Barbara Peplies found among her brother's belongings.

"When we discussed issues with the inspectors, we got the impression they weren't doing anything," Barbara says. "They seemed to have concluded that Bert had murdered Linda and then committed suicide. My brother knew a lot of shady people, and Inspector Lynch wasn't interested in speaking to any of them. I don't think she cared about investigating this case. She was very cold."

Diane Rigda, who is married to Robert Peplies' stepbrother, says the most important thing for the family is to know what happened. "It's a very big difference whether Bert killed and committed suicide, or was killed by a third person," she says. "It's a big difference, and it would be comforting to have some answers. We've been so upset for the last year not knowing."

More than a year later, police say Peplies' autopsy is still not ready. The delay has been frustrating for the family, because there's a chance the autopsy and crime scene report could answer questions about what happened in the Sargent Street home.

The crime scene report should have fingerprint analysis on the bloody pipe and knives. It may also reveal if there were bloody footprints in the home other than Peplies'. The autopsy may be able to determine whether his wounds were consistent with self-stabbing, or if he had defensive wounds to his hands and forearms. But perhaps most importantly, it should contain critical DNA results. Linda Almanza's killing was so brutal that whoever killed her would likely have been covered in her blood. If the results show her blood was not on Peplies' hair, body, or clothing, there is a strong possibility he did not kill her. And, more chillingly, such a result could mean one or more particularly brutal murderers are still on city streets.

As in the Schirra case, the informational linchpins in the Peplies-Almanza case are the autopsies. The police and the medical examiner will not release any information about the case until the autopsies are complete.

The fact that the autopsies have yet to be completed more than a year after these deaths is troubling, medical and criminal experts say. "The standard time for autopsy reports is 30 days to 60 days," says Dr. Jeffrey Jentzen, president of the National Association of Medical Examiners. "There are cases where they take longer if there's complicated toxicology, brain, or cardiac examinations required."

Former Alameda County Sheriff Charlie Plummer, who served five terms as sheriff and ran the coroner's office, was more direct. "That's bullshit," he says. "They're selling you a line of crap. We contracted for a pathologist in Alameda, and if it took that long to turn around an autopsy, the contract would have been canceled." Both Stasko and chief medical examiner Hart have refused to say what is causing the delay, but a forensic pathologist in the medical examiner's office told a Peplies family member that the office is waiting for DNA results. Neither the police nor medical examiner would say where the DNA was being analyzed, but the majority of the city's testing is done by the SFPD's crime lab. Crime lab forensic services director Cydne Holt did not return calls to SF Weekly asking whether her division was analyzing the DNA from the Peplies and Schirra cases.

The crime lab, which is under the purview of the police department, has had a troubled history of not keeping up with its workload. It receives an estimated 14,000 annual requests to analyze evidence that includes chemicals, narcotics, breath alcohol results, firearms, documents, and, of course, DNA evidence from rape, assault, and homicide cases. A 2003 Legislative Analyst Report found the crime lab was understaffed and underfunded compared to other labs. It had a backlog of more than 500 DNA cases. At the time of the report, DNA cases took an average of six months and some as long as 10 months.

Rigda says she is unsympathetic to stories of overwhelmed police laboratories, and that dealing with the SFPD over the last year has been a rude awakening. "There's been so much stonewalling, it's made me question whether they are trying to cover something up," she says. "The idea that the authorities will do everything they can to figure out what happens when someone dies like this is very, very comforting. We have not had that feeling in this case at all."

Poorly handled homicide cases are nothing new in the San Francisco Police Department. In 2002, the San Francisco Chronicle published a three-part series on the department's substandard violent crime investigations. The series depicted a homicide detail hamstrung by lax policies, promotion standards that favor mediocrity, embarrassingly low solve rates, scant resources (homicide inspectors did not have city e-mail accounts or Internet access until last year, according to Inspector Tom Walsh), and poor oversight.

And, unsurprisingly, the homicide detail had the third-worst clearance rates of 20 other similar-sized cities. Using a five-year average, the Chronicle determined that the homicide detail cleared 50 percent of the homicides, while other large cities cleared an average of 61 percent. According to FBI criteria, a case is considered to be cleared when an arrest is made or a suspect dies, is incarcerated, or extradition is denied. Whether a suspect is actually charged doesn't matter.

Homicides in San Francisco have increased since 2000, when there were 59. In the last four years the annual number has been in the high 90s, except for 2006 when it dipped to 85. As of September 5, there have been 73 homicides in San Francisco. Of the 98 homicides in 2007, inspectors cleared 25 percent of the cases compared to the statewide average of 53 percent, according to California Department of Justice statistics.

As chairman of the Public Safety Committee, Supervisor Ross Mirkarimi has been a vocal critic of the homicide detail's poor clearance rate and its treatment of victims' families. But he has also defended the bureau by shifting responsibility to Mayor Gavin Newsom, who he says has the power to fix the problems. "It's unacceptable," Mirkarimi says. "The city needs to upgrade all levels of customer service, especially when it comes to something so profoundly heartbreaking as murder. The only person who can fix the problem is the mayor, and instead there seems to be a great effort to avoid the subject because of the effect it could have on one's political ambition."

One problem, Mirkarimi says, is Chief Heather Fong. It has been widely speculated that Newsom, who has begun to collect campaign contributions for a possible run for the governor's office in 2010, is reluctant to fire her because it might alienate Asian voters. Newsom's press office did not return numerous calls and e-mails seeking comment for this story. Nor did Fong, who is known for avoiding the press and cultivating an air of secrecy around her office (see SF Weekly, "The Chief Is In (for Now)," Aug. 6).

One case that demonstrated a lack of departmental accountability was the bizarre death of Hugues de la Plaza. De la Plaza was found dead in his apartment with one stab wound to his throat and two to his torso. When homicide investigators seemed to be in a rush to classify the case as a suicide, even though they found no bloody knife in the apartment, they were not prepared for de la Plaza's ex-girlfriend, Melissa Nix.

Nix is an experienced journalist who covers an education beat for the Sacramento Bee. As a reporter, she is unintimidated by bureaucracy and has a working knowledge of government accountability. Along with a committed group of de la Plaza's friends, she was relentless in pursuing a 16-page list that contained 13 detailed complaints about such things as neglected witnesses, a lack of fingerprint analysis and technical expertise, false information leaks to the press, and poor communication with the de la Plaza family.

Nix took her complaints to the department's command staff, the Police Commission, the Office of Citizens' Complaints, the Mayor's Office of Criminal Justice, and the mayor's office itself, though the mayor refused to speak with her or the family. "It's a problem of leadership," she says. "I don't know how Gavin Newsom thinks he's going to be elected governor with that kind of record on crime." Nix also took her case to the media (see SF Weekly, "Who Killed Hugues de la Plaza?," July 18, 2007); the story later ran in the Chronicle, The Washington Post, and People magazine.

A federal court stepped in and ordered that a French judge should be allowed to subpoena witnesses and that the San Francisco Police Department should turn over the forensic evidence to French investigators, who have taken it back to Paris. Fong held a rare press conference to claim the SFPD was conducting a parallel investigation and insisted the French authorities were not taking over the case. But Board of Supervisors President Aaron Peskin called the handoff "simply outrageous," and Mirkarimi says it was a clear sign the police department needs a change. "I like Chief Fong, but she has been chief for four years, which exceeds most chiefs," he says. "So the question is begged to the mayor, why not make a change when homicides and violent crime have gone so wrong? All the mayor is doing is biding time until he can fire her without offending certain constituencies."

One high-ranking police officer who asked not to be identified says the department is still confident that ultimately the de la Plaza investigation will show the Frenchman committed suicide. "As goofy as that case is, we're certain the suicide theory will pan out," he says.

Criminology professor David Klinger says that police could be correct in their four murderless stabbing theories. "Someone can commit suicide with a knife and throw it off a balcony onto a roof or in the street, where someone could pick it up," he says. "The mere fact that someone is found stabbed to death and there is no knife does not mean it's a fabulous suicide."

But Klinger says when police are faced with solving such bizarre cases, their credibility means everything with the families' confidence in their theories. "If you have a homicide inspector with years of experience and a reputation for being straightforward and thorough, you're going to give a great deal of weight to his theory," he says. "But if you have a police department with a history of bad recordkeeping, poor collection of evidence, and sloppy investigations, you're not going to have much confidence in what they say."

Barbara Peplies says she is waiting to be confident. She always felt protective of her younger brother. After Bert died, she felt helpless when homicide inspectors appeared to lack interest in solving the case. She traveled to San Francisco, but did not know what to do. She wanted to see the house he died in, but inspectors would not tell her where it was. Out of frustration, she went down to Van Ness and Market and approached people who looked like heroin addicts, on the remote chance they knew him or had heard about the murders in Ingleside Heights. "They were all very nice, but none of them knew him, of course," she says. "I know it was a stupid thing to do."

Shortly after Peplies returned to Tennessee, where she works as a dietician, she went to an emergency room because she was overwhelmed with stress. She still thinks about her brother all the time, and says it has affected her work. "I don't want to think of him as a murderer, but I could accept it if there was some real proof," she says. "But there's nothing we can do until we get hard facts, and we've been waiting."

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