CIUDAD JUAREZ, Mexico—The hit men moved in on their target, shot him dead and then disappeared in a matter of seconds. It would have been a perfect case for Jose Ibarra Limon, one of this violent border city's most dogged crime investigators—had he not been the victim.

Mexico has never been particularly adept at bringing criminals to justice, and the drug war has made things worse. Investigators are now swamped with homicides and other drug crimes, most of which they will never crack. On top of the standard obstacles—too little expertise, too much corruption—is one that seems to grow by the day: outright fear of becoming the next body in the street.

Ibarra was killed on July 27 in what his bosses at the federal attorney general's office consider an assassination related to a case he was investigating. As if to prove the point, less than a month later, one of the lawyers who had worked for Ibarra also turned up dead. Two days afterward, an investigator named to replace Ibarra insisted on being transferred out of Ciudad Juarez, Mexico's murder capital.

The current prosecutor investigating Ibarra's cases is working anonymously, his or her name kept secret by the government.

The Mexican government knows that revamping its justice system is an essential part of breaking the cartels that control vast areas of Mexico. Major efforts are under way to make the judiciary faster and fairer, and the United States has contributed millions of dollars to help bring more criminals to justice.

But even with training programs by American lawyers and judges, American aid to improve forensics and screen more effectively for corruption, as well as other cross-border initiatives, the traffickers and the cumulative pressures they are putting on the judiciary are straining it as never before.

“;Obviously what happened affects us,”; said Hector Garcia Rodriguez, the federal prosecutor in Juarez and the supervisor of the slain investigator. “;We're still working. We can't stop. But we know the dangers we face.”;

President Felipe Calderon points to the arrests of more than 50,000 people on drug charges since he began his antidrug offensive in December 2006. Many of the arrests appear to have come from top-notch detective work. Other suspects, though, are quietly released after they have been paraded before the news media.

The federal government refused to provide statistics on how many arrests had resulted in convictions, how many suspects were still under investigation or how many arrests had proved to be mistakes. But independent reviews by scholars suggest that only about a quarter of crimes in Mexico are ever reported and that only a small fraction ever result in convictions.

Compounding matters is the sheer number of crimes, especially murders. On a single September night in Ciudad Juarez, 18 men were shot to death in a drug treatment center near the border, more than the number of killings all year long in El Paso, Texas, just across the border.

“;Law enforcement is overwhelmed,”; said David A. Shirk, a professor at the University of San Diego and the principal investigator for the Justice in Mexico Project, a binational research initiative. “;If you have murders with 13 bodies one day and then you have four more the next, there's not a lot of investigation into who pulled the trigger specifically.”;

One of the two dozen or so cases that Ibarra had been investigating involved the killing of a journalist, Armando Rodriguez Carreon, 40, who had produced a string of scoops as the longtime crime reporter for the newspaper El Diario. Rodriguez was shot to death last Nov. 13 as he prepared to take his 8-year-old daughter to school. She was at his side and saw her father struck with at least 10 bullets.

“;It was similar to hundreds of homicides we've had here,”; remarked Garcia, Ibarra's supervisor. “;It was an execution.”;

It is also similar in that the perpetrators remain at large. Fear prevents many cases from being solved because investigators hesitate to dig too deeply, and witnesses refuse to talk.

“;Nobody cooperates with anything,”; Garcia complained. “;They're too afraid. Nobody wants to say what they saw. Nobody wants to give you a plate number.”;

Mexico is promoting confidential telephone lines and rewards to encourage witnesses, but resistance lingers, especially when news reports circulate about threats made to those who do call in. And there is considerable doubt that the reward money is worth the risk.

The attacks on investigators only magnify the problem.

“;If you had a difficult case, you went to him and said, 'Ibarra, what do you think?”;' Garcia said. Now in trying to solve Ibarra's murder, his colleagues wonder aloud how he might have pursued his killers, possibly four men in all, who shot him numerous times in the head with .45 caliber and 9 mm weapons.

The slain journalist's wife, Blanca Martinez, said that she had met once with Ibarra, but that she did not think he had been murdered for closing in on her husband's killers, despite his reputation for solving difficult crimes.

“;I don't think he was really investigating,”; she said. Prosecutors had asked once to interview her young daughter, a witness, but had never followed up, Martinez said.

Pedro Torres, Rodriguez's editor and close friend, was similarly unimpressed with the government's effort to find the killers of his top police reporter.

Investigators waited for months before visiting the newsroom, interviewing some of Rodriguez's co-workers and getting copies of his articles. The government has not yet established whether Rodriguez's killing stemmed from his work as a police reporter, infuriating his colleagues, who are convinced that such a connection is clear.

“;He's the godfather of my child,”; Torres said. “;I've known him for years. They've never talked to me. What kind of investigation is that?”;

One of the forensic specialists who photograph bodies, lift fingerprints and count spent bullets at Juarez homicide scenes complained that by the time he arrived at a site, significant tampering had already taken place.

“;The soldiers come in and walk over everything,”; complained the specialist, who spoke anonymously in an out-of-the-way steak restaurant because his supervisors had not authorized him to give an interview. “;They leave their fingerprints all around. They want to know who died, so they move the body. They kick the bullets. They don't realize they're contaminating the crime scene.”;

Thousands of soldiers, deployed by the president in his war against the cartels, patrol the streets of Juarez alongside the local police. Trained to take on enemy combatants, they are far less familiar with the sanctity of crime scenes, the rules of evidence and other basics of law enforcement.

Many police officers also meddle with crime scenes, sometimes out of incompetence, but sometimes to throw off the investigation or to enrich themselves.

“;If the victim's watch is missing, that could be important because it could mean it was a robbery,”; the forensic specialist said. “;But we can't rule out that one of the police officers at the scene took it.”;

The joint military-police mission combating traffickers in Juarez presents a more positive picture. It cites the recent arrests of three men suspected of being hired killers, who in August implicated themselves and a fourth suspect in 211 homicides, an eye-popping number even in Mexico.

To trumpet the breakthrough, the government took out newspaper ads listing all the people the suspects were accused of killing. One man alone was linked to 101 murders.

The authorities said the arrests resulted from ballistics investigations, which are modern enough here in Chihuahua State that the El Paso Police Department used them for years for its own investigations. But the men also confessed to the murders, the authorities said, and questions were raised in the local news media about whether the detainees had been coerced, a frequent problem in Mexico.

“;We solve our crimes with evidence, and they solve them with confessions,”; said the El Paso County sheriff, Richard D. Wiles. “;We have strict rules to follow on how to get confessions. The rules are looser over there.”;

In a recent assessment of Mexico's adherence to human rights, the State Department noted that 21 torture complaints and 580 complaints of cruel or degrading treatment had been made against the Mexican authorities in 2008, a significant increase from the year before.

And yet, “;since 2007, we are not aware that any official has ever been convicted of torture, giving rise to concern about impunity,”; the report said. “;Despite the law's provisions to the contrary, police and prosecutors have attempted to justify an arrest by forcibly securing a confession of a crime.”;

Garcia, the Juarez prosecutor, says coercion is not what prompts so many confessions, since many of the hardened traffickers are eager to claim credit for their acts. “;They confess because they feel good about what they did,”; he said.

Along the border, many victims are never found, leaving relatives—and investigators—in limbo.

Fernando Ocegueda Flores, a founder of an advocacy group in Tijuana for relatives of the disappeared, felt an odd mixture of despair and relief in January, when the police announced that a suspect, Santiago Meza Lopez, had admitted to disposing of the remains of 300 bodies for a drug cartel by dissolving them in barrels of lye.

Ocegueda thought that maybe his son, abducted in 2007, had been one of the victims of the Pozolero, a nickname for Meza that translates roughly as the stew maker. Ocegueda thought his years of trying to learn his son's fate might end.

Federal authorities took Meza to Mexico City for questioning and began testing some remains. But the bones were so corroded by the lye that no DNA was found, the authorities have said.

Ocegueda contends that the investigators should be doing more, like digging up the yard where Meza said he had disposed of the bodies after boiling them, to search for more bones to test. The yard is guarded by the federal police, but a human jaw bone with a tooth attached and various suspicious mounds of earth were visible from a peek inside.

Frustrated, Ocegueda said that if the site was not properly investigated soon, he and other relatives planned to storm the place with shovels and begin digging themselves.

But a coroner's investigator who has reviewed some of the remains from such barrels in other cases said the traffickers covered their tracks well.

“;You can't tell by looking that it's a human being,”; said the investigator, who was not authorized to speak publicly. “;It's a glob of something, and the DNA is gone.”;

Every month, law enforcement officials from both sides of the border, whether from the FBI or the Tijuana police, gather to talk shop at a chain restaurant in southern California.

“;Without cooperation, so many cases would sit still,”; said the California investigator who convenes the sessions, Val Jimenez, executive director of the International Law Enforcement Officers Association. Cross-border policing has caught child molesters, car thieves and murderers.

It also helped solve one particularly grisly missing person case.

Daniel LaPorte, 27, disappeared after heading across the border to Baja California from San Diego last year. Eventually, his green Cadillac was found south of Tijuana, outside Rosarito Beach, with four dead people in and around it. None were LaPorte.

As the family's private investigator looked into the case with police officers from San Diego and Baja California, a Mexican detective mentioned that a barrel apparently containing human remains had been discovered not far from the location of the quadruple homicide.

Luck played a role in identifying the remains. It had rained heavily after the barrel had been abandoned on a remote hillside, investigators said. The barrel had fallen over and some of the bones had been washed away by the rain, diluting the corrosive solution and preventing all the DNA from being stripped away. Laboratory tests conducted in Tijuana showed that the remains were LaPorte's.

Investigators eventually determined that LaPorte had been involved in trafficking marijuana from Mexico to Rhode Island, some of it in surfboards. He had probably bought several tons of marijuana a year, the family's investigator said.

Jimenez and some of the other law enforcement officials who work on these joint investigations are sympathetic to the policing challenges their Mexican counterparts face.

“;We don't think we're going to die when we go to work, but over there it is a real possibility,”; Jimenez said. “;A lot of them want to do good police work, but there are some cases they can't do because of the pressure of the cartels.”;

Alejandra Gonzalez Licea said the only conceivable ties she had ever had to drug trafficking were purely academic ones. A linguistics professor who wrote her thesis on narcocorridos, the Mexican ballads that often extol the exploits of drug bosses, Gonzalez found herself blindfolded and handcuffed by soldiers this year and grilled about which drug cartel was employing her.

Her answer—the Autonomous University of Baja California—did not impress her interrogators. The professor and her husband endured months of detention before the charges were quietly dropped. The $28,000 in cash they were caught carrying was a gift from an uncle in the United States to help them remodel their home, it was determined, not illicit drug profits they were laundering.

After her initial detention, Gonzalez was led to a news conference, where journalists were gathered to photograph her. She stood next to her husband and two men she did not know. On the table before them, much to her surprise, was nearly half a million dollars.

It turned out that she was being grouped with two money laundering suspects arrested the same night with a much larger amount of cash. It would take two and a half months before a judge would throw out the case against her and her husband for lack of proof.

Mexico has approved a sweeping overhaul of its judiciary to replace its closed-door judicial proceedings with trials in which defendants like Gonzalez are considered innocent until proved guilty. But revamping the system is no easy feat. It requires retraining lawyers and judges, rebuilding courtrooms and improving forensic technology, all while trying to keep on top of a flood of new cases.

Police forces are also getting an overhaul. Officers in Tijuana and Juarez, two of the most violence-prone cities, have been fired en masse after being linked to organized crime. The two federal police agencies have been reorganized under a single commander. Beyond that, a new police training institute has been established and the government has set up a national database to share information and intelligence.

Still, Gonzalez, now back at her teaching job, shook her head when asked about the Mexican government's competence. She doubts the official statistics, since she figures she was one of the 50,000 people that the president cited as drug suspects.

“;They didn't even find out that I wrote my thesis on narcocorridos,”; she said of those who were prosecuting her. “;Good thing they didn't find out.”;

The authorities discourage civilians from investigating their own cases because of the obvious dangers involved. But many grow tired of waiting for the police and, having no luck with private investigators, conduct their own inquiries.

Christina Palacios, president of the Citizen's Association Against Impunity, recounted how one of her members, a Tijuana woman whose brother had been kidnapped, offered a reward herself, furious at how little had be done to investigate the disappearance .

Shadowy men contacted the woman, and she agreed to be taken away with a blindfold, said Palacios. Soon the woman found herself in a room, where there was a man tied to a chair being beaten by a group of men. The man confessed to killing her son.

The next day, the woman, who declined to speak on the record about what occurred, saw in the newspaper that a body had been found. It looked like the man in the chair, Palacios said.

Ocegueda, in search of his missing son, had a similar experience. One night, in the course of his personal investigation, he allowed himself to be led away with his eyes covered and driven for about 40 minutes by a man he met who had links to traffickers.

Eventually, he was led into a home, where he said a gruff man told him, “;You're very brave to come here.”;

Apparently impressed by his gumption, the man gave Ocegueda a shot of whiskey and told him that his son had been killed and would never be found. His remains had been destroyed in lye, the man said.

But Ocegueda, continuing to investigate, later found another organized crime figure, who led him in another direction. This time, he was told his son was alive and working for traffickers. Now, he does not know what to think.

“;The police are supposed to be doing this, not me,”; he said. “;But they don't want to investigate because they don't want to solve these crimes. They might be killed if they find the truth. I don't care if they kill me.”;