The national furor has subsided for the moment. But as the second-degree murder case against the defendant, George Zimmerman, moves from the glare of a public spectacle to the grinding procedures of the court system and eventual trial, the department’s performance, roundly criticized by Mr. Martin’s family as bungling and biased, will be scrutinized once again, though in more meticulous detail.

With doubts shadowing the quality and scope of the police work, the prosecution and the defense will be left to tackle critical questions even as they debate the evidence. And ultimately, what happened on the rainy night of Feb. 26 may come to rest on the word of one man, George Zimmerman, the 28-year-old neighborhood watch volunteer who fired the fatal shot.

In interviews over several weeks, law enforcement authorities, witnesses and local elected officials identified problems with the initial investigation:

¶ On the night of the shooting, door-to-door canvassing was not exhaustive enough, said a law enforcement official familiar with the investigation. If officers had been more thorough, they might have determined that Mr. Martin, 17, was a guest — as opposed to an intruder — at a gated community called the Retreat at Twin Lakes. That would have been an important part of the subjective analysis that night by officers sizing up Mr. Zimmerman’s story. Investigators found no witnesses who saw the fight start. Others saw parts of a struggle they could not clearly observe or hear. One witness, though, provided information to the police that corroborated Mr. Zimmerman’s account of the struggle, according to a law enforcement official.

¶ The police took only one photo at the scene of any of Mr. Zimmerman’s injuries — a full-face picture of him that showed a bloodied nose — before paramedics tended to him. It was shot on a department cellphone camera and was not downloaded for a few days, an oversight by the officer who took it.

¶ The vehicle that Mr. Zimmerman was driving when he first spotted Mr. Martin was mistakenly not secured by officers as part of the crime scene. The vehicle was an important link in the fatal encounter because it was where Mr. Zimmerman called the police to report a suspicious teenager in a hooded sweatshirt roaming through the Retreat. Mr. Zimmerman also said he was walking back to the vehicle when he was confronted by Mr. Martin, who was unarmed, before shooting him.

¶ The police were not able to cover the crime scene to shield evidence from the rain, and any blood from cuts that Mr. Zimmerman suffered when he said Mr. Martin pounded his head into a sidewalk may have been washed away.

¶ The police did not test Mr. Zimmerman for alcohol or drug use that night, and one witness said the lead investigator quickly jumped to a conclusion that it was Mr. Zimmerman, and not Mr. Martin, who cried for help during the struggle.

Some Sanford officers were skeptical from the beginning about certain details of Mr. Zimmerman’s account. For instance, he told the police that Mr. Martin had punched him over and over again, but they questioned whether his injuries were consistent with the number of blows he claimed he received. They also suspected that some of the threatening and dramatic language that Mr. Zimmerman said Mr. Martin uttered during the struggle — like “You are going to die tonight” — sounded contrived.

The Sanford police — who contended that their 16-day investigation, done in consultation with the original prosecutor in the case, was detailed and impartial — also encountered other obstacles. One involved the investigators’ inability to get the password for Mr. Martin’s cellphone from his family, who apparently did not know it. That was significant because Mr. Martin had been talking to a girl on the phone moments before he was killed, but the young woman did not contact the police after Mr. Martin’s death was made public.

From what is known of the investigation and the available evidence, what exactly happened in the dimly lighted residential development that Sunday night may remain out of reach. Given Mr. Zimmerman’s assertion that he was acting in self-defense, and lacking enough evidence to the contrary, the original prosecutor in the case, Norm Wolfinger, whose jurisdiction includes Sanford, filed no charges against him.

That decision resulted in an increasingly strident public outcry. After Gov. Rick Scott of Florida contacted Mr. Wolfinger and had a conversation with him in late March, the prosecutor recused himself, citing, among other things, an unspecified conflict of interest.

The governor selected another state attorney to handle the case, Angela B. Corey of the Jacksonville area. On April 11, after nearly three weeks of investigation, Ms. Corey charged Mr. Zimmerman with second-degree murder. An accompanying affidavit said that Mr. Zimmerman had “profiled” Mr. Martin and had assumed he was a criminal.

Ms. Corey declined to be interviewed, as did Mr. Wolfinger. Governor Scott also declined several requests for an interview about how and why he selected Ms. Corey for the case.

In announcing the charge, Ms. Corey praised the Sanford Police Department’s work, indicating that it had conducted a “thorough and intensive” inquiry and was a “tremendous help” to her office. Eight Minutes

What appears unchanged since the beginning, however, is that investigators say they do not know who started the fight. Florida’s controversial Stand Your Ground law, which has come to shadow a number of homicide cases since it was adopted in 2005, justifies the use of deadly force in certain threatening situations but does not require a person to retreat. The law became the framework within which the police and prosecutors had to work after Mr. Zimmerman claimed that Mr. Martin confronted and pounced on him.

Mr. Zimmerman had called the police from his vehicle to report what he believed was a suspicious person in the Retreat, something he had done numerous times in the past. He later told investigators that he got out of his vehicle and followed Mr. Martin but lost sight of him. As Mr. Zimmerman was returning to his vehicle, he told them, Mr. Martin emerged and then attacked him. Mr. Zimmerman told investigators that at one point, Mr. Martin had his hand over his mouth. And before he shot the youth, he explained to the police, Mr. Martin had reached for Mr. Zimmerman’s gun.

“There is a perception that we were trying to protect George Zimmerman,” the Sanford police chief, Bill Lee Jr., who temporarily stepped aside in March to quell the furor and later offered to resign, said in a recent interview. “We think that what he did was terrible. We wish that he had just stayed in his vehicle.”

“There was no bias in the investigation. We did not lean one way or another. We were looking for the truth,” he said.

Chief Lee declined to discuss specifics about the case, but he added, “I have been frustrated by the negative attention the police and the city have received that does not accurately reflect who we are and what we have done in this investigation.”

At 7:09 p.m., Mr. Zimmerman, who was driving to a Target store, made his call to a police dispatcher.

Within eight minutes, Mr. Martin was dead from a gunshot wound to the chest, his body crumpled on a stretch of grass behind a row of town houses. When the first officer arrived at 7:17, Mr. Zimmerman was waiting not far from the body. He raised his hands in surrender before relinquishing his 9-millimeter pistol from the holster in his waistband.

He was handcuffed and taken into “investigative detention” at Sanford police headquarters, where he was read his Miranda rights and answered questions without a lawyer present. Investigators described him as unhesitatingly cooperative. At some point, Mr. Zimmerman provided the police with a permit allowing him to carry a concealed weapon. His clothes were taken into evidence after his wife came to the station with a new set.

A law enforcement official said officers did not seize Mr. Zimmerman’s vehicle because they thought that he had been on foot. They did not realize that he had been driving until after his wife had moved the vehicle, the official said.

The official said he believed that the police, in the hours after the shooting, sought to determine whether Mr. Zimmerman was wanted for any crimes. But he said they did not have a complete background check in hand until midmorning the next day — after Mr. Zimmerman had been released. The records showed a domestic violence dispute with a woman who identified herself as his ex-fiancée and a run-in with a state alcohol agent, neither of which resulted in a conviction.

As for the officer at the scene who took the single full-face photo of Mr. Zimmerman — he suffered a nose fracture and other injuries during the struggle — he called an investigator “in a panic” over his failure to download it sooner, according to a person familiar with the case. Other photos of Mr. Zimmerman’s injuries were later shot at police headquarters, although he had been cleaned up by paramedics by then.

Another investigator briefed on the case said officers should have been more thorough as they knocked on doors in the neighborhood: they might have learned Mr. Martin’s identity early and that he was staying at the town house of his father’s girlfriend and was not trespassing. At the time of the shooting, the girlfriend’s 14-year-old son was waiting for Mr. Martin to return from a 7-Eleven store, where he had bought a bag of Skittles candies and a can of iced tea. Mr. Martin was not identified until Monday morning, about 12 hours after he was killed, when the police learned that his father, Tracy Martin, had reported him as missing.

One witness said a police investigator twice declined her offer to show him the close and unobstructed vantage point from a partly opened bedroom window where she had watched and heard the struggle between Mr. Martin and Mr. Zimmerman. The witness, who agreed to be interviewed on the condition she remain anonymous because the investigation is active, said the detective taped part of her account.

She also recalled telling him that night that she was haunted by the cries for help she believed came from Mr. Martin during the struggle. But she said the investigator seemed to have already formed an opinion about what had happened. He told her, she said, that it was Mr. Zimmerman — not Mr. Martin — who was the one screaming, an assertion that remains in dispute.

More than a month later, she and her lawyer, Derek Brett of Orlando, met with two investigators from Ms. Corey’s office. Mr. Brett said his client was subject to only 15 minutes or so of “substantive questioning.”

“This surprised me because when something is not done properly, in this instance by the police, you sit down and do more than just fill in the blanks,” he said.

On the night of the shooting, the police were assisted by the Seminole County sheriff’s office, which sent a representative to the scene with a live fingerprint scanner to see if a match showed up for Mr. Martin. It did not.

Benjamin Crump, a lawyer for the Martins, said that Mr. Martin was carrying a T-Mobile Comet phone and that the police contacted his father a day or two after the shooting to get the password, but he did not know it.

A law enforcement official said that the phone had died not long after the police retrieved it, and that it took days for the authorities to get a charger and an expert to try to get into the device. If the police had been able to get access to it, they could have interviewed Mr. Martin’s friend about what he had told her in those final moments of his life and what else she had heard. The police eventually subpoenaed Mr. Martin’s cellphone records, but did not receive them in a timely fashion.

The official said that while the police never tested Mr. Zimmerman for alcohol or drugs, such decisions are left to the discretion of investigators based on whether they have reason to suspect the person is under the influence. (The medical examiner in the case did a routine toxicology screening of Mr. Martin; the results have` not been made public.)

Sgt. David Morgenstern, spokesman for the Sanford police, said he could not say much about the case because the investigation was continuing. But he said of the officer who took one photo of Mr. Zimmerman at the scene: “I don’t think that is wrong because subsequent photos can be taken within hours. They might not be as graphic but they still will depict the injuries somebody might have.”

Over all, Chief Lee, whose resignation was not accepted by the City Commission last month, said in an interview that his department’s work was as fair and thorough as possible.

“I am confident about the investigation, and I was satisfied with the amount of evidence and testimony we got in the time we had the case,” he said.

“We were basing our decisions, which were made in concert with the state attorney’s office, on the findings of the investigation at the time,” he added, “and we were abiding by the Florida law that covers self-defense.”

Sorting the Evidence

The Sanford Police Department assigns homicide cases to its five investigators who handle major crimes. Their wide-ranging responsibilities cover everything from sex crimes to carjackings. On the evening that Mr. Martin was fatally shot, the head of the major crimes unit was on vacation. The rotation supervisor on call was a sergeant who works narcotics cases. In all, more than a dozen officers and department superiors were on the scene of Mr. Martin’s killing — which the police said was Sanford’s first homicide of 2012 — including Chief Lee, who joined the department last May.

In the two weeks after the shooting, the police were in regular contact with the office of Mr. Wolfinger, sharing their findings and suspicions with him.

The police conducted a lie-detection procedure, known as voice stress analysis, on Mr. Zimmerman that he passed, and they had him re-enact the encounter with Mr. Martin back at the Retreat the day after the shooting. But the operating belief was that the police did not have enough evidence to establish probable cause for a manslaughter charge and an arrest, according to officials with knowledge of the case.

At one department meeting a few days after Mr. Martin’s death, a representative from Mr. Wolfinger’s office was told about the inconsistencies the police saw in Mr. Zimmerman’s account. The prosecutor told them he understood that the police were trying to build a case against Mr. Zimmerman, though they did not have adequate evidence, according to a law enforcement official. It was decided that more work was needed on the case.

As the national uproar intensified, the Sanford city manager, Norton N. Bonaparte Jr., and Mayor Jeff Triplett were growing eager to have the police send the case to Mr. Wolfinger to get it moving through the justice system. The police did so just over two weeks after Mr. Martin’s death. They included a recommendation that Mr. Zimmerman be charged with manslaughter, a position that one law enforcement official described as “weak,” and that the prosecutor did not act on.

Ms. Corey’s decision to charge Mr. Zimmerman with second-degree murder fueled even more criticism of the police. Mr. Zimmerman has since entered a written plea of not guilty.