The alleyway where Victor Ortega died, the one that cuts up the middle of Court 84 of the Mesa Village apartments in Mira Mesa, is a little more than 3 feet wide. Enclosed by a high stucco wall on one side and a fence on the other, it’s a cramped space. It’s where, on the morning of June 4, 2012, San Diego police officer Jonathan McCarthy shot and killed the 31-year-old unarmed father of two after Ortega allegedly grabbed for the officer’s gun.

Townhouses surround the alley, but there were no witnesses to Ortega’s death. Two residents told investigators they saw, from their window, McCarthy and Ortega engaged in a struggle, but turned away seconds before shots were fired. Several other people reported hearing Ortega say a stunned “Are you kidding me?” and “I’ll sue you” moments before gunfire.

McCarthy, who had spent just two years on the force before the incident, told police investigators that he feared for his life before he shot Ortega. Based on the officer’s version of events, prosecutors said Ortega’s killing was justified.

But police reports, depositions, interview transcripts and other evidence disclosed in a federal lawsuit filed two years ago by Ortega’s widow reveal inconsistencies in McCarthy’s account of what happened in the alleyway immediately before Ortega’s death. U.S. District Court Judge Larry Burns, who is presiding over the case, recently expressed doubt that it would be possible for McCarthy to have done everything he said he did during his altercation with Ortega.

In denying the city’s request to throw out the lawsuit, the judge ruled that McCarthy’s story has enough holes that a jury needs to sort out what happened.

“Plaintiffs,” Burns wrote, “have submitted evidence that would give a reasonable jury pause.”

Ortega was killed almost three years ago, but his case shares some of the same characteristics as other disputed police shootings that have recently inflamed communities across the country. A police officer pursued an unarmed criminal suspect. A struggle ensued with conflicting evidence about what occurred. And the suspect ended up dead.

In Ortega’s case, everything began with a call to 911.

Victor and Shakina Ortega were together for 11 years, married for eight. A mutual friend introduced them. “We just clicked,” Shakina said. Their daughter Tamia was born in 2006 and son Jacob five years later.

Victor was the sensitive one in the relationship, a good dad and a family guy, Shakina said. He’d take Tamia on play dates and have dinner ready when Shakina returned from work. “He wore his heart on his sleeve,” she said. Shakina, on the other hand, is serious, no-nonsense. She held down a full-time job, working as a ride operator at SeaWorld, while he struggled to find consistent work as a mover. This was a source of frustration in their marriage that led to arguments, like the one on June 4, 2012.

On that day, just after 7:30 a.m., Shakina called 911. She told the dispatcher that her husband had hit her and her mouth was bleeding. She initially said she needed an ambulance, but quickly corrected herself to say she needed the police. She told the dispatcher Victor had become angry after she woke him to demand he take Tamia to school.

A little more than a year later, in a deposition, Shakina said she had overreacted. She was tired, she said, and she’d lost her temper. She had yelled, thrown things at him and then sat down on the edge of the bed. When Victor kicked off the bed covers, his foot hit her upper lip, she said, causing it to start bleeding.

Angry, she told him she was calling the police. She’d called 911 on him before when the two of them would argue. Sometimes she’d pretend to call 911. On the morning of June 4, she says now that she thinks Victor probably suspected it was another one of those pretend calls. Shakina’s sister had already taken Tamia to school so Victor got dressed and left the house to give Shakina time to calm down.

About 15 minutes after Shakina’s call to the police, McCarthy and Officer Godfrey Maynard arrived at the couple’s home in separate cars.

When they pulled up, Shakina was standing outside. She told the officers that Victor had left.

McCarthy later told homicide investigators that he and Maynard decided to split up and search for Victor. Shakina said neither officer interviewed her nor checked to see if she was OK. McCarthy later testified that she appeared uninjured.

McCarthy told investigators that he drove to the end of the block and made a right turn. A few driveways up, he saw a man who fit Ortega’s description: 31 years old, tall, thin and wearing black shorts. McCarthy said that when Ortega spotted him, he took off running. McCarthy got out of his car and gave chase, radioing in the pursuit to his colleagues.

Less than a minute later, Ortega would be dead.

Several residents told police investigators they heard McCarthy yell at Ortega to stop running. One resident saw the two men run by “in a blur.” At some point, Ortega, who’d been heading eastbound, turned and ran through an open gate, into the alleyway, and closed the gate behind him.

McCarthy kicked open the gate. He saw Ortega in the alley.

Ortega was walking away but looking back at him, McCarthy told investigators. He said he ordered Ortega to get on the ground and when he wouldn’t comply, used physical force.

“We start pushing each other,” McCarthy told investigators, “we’re bumping against the walls.”

McCarthy said he used a leg swipe to knock Ortega to the ground.

As for what happened next, McCarthy’s provided multiple versions. In at least two accounts, he said he’d pulled out his Taser and warned Ortega he was about to use it. In another, he didn’t mention the Taser at all. No witnesses recall hearing McCarthy say anything about a Taser and the two eyewitnesses didn’t recall seeing one. Instead, they reported hearing a command to “get down” and another voice – Ortega’s – saying, “What are you doing? Get off me,” “Are you kidding me?” and “I’m going to sue you.”

A witness who heard the altercation told investigators that the tone of Ortega’s voice was “one of compliance and disbelief, not confrontational or violent.”

The two eyewitnesses to the fight don’t provide clarity. In initial interviews with police, one man said he didn’t see much, though in his later deposition said the struggle between McCarthy and Ortega was intense and unabated. The second eyewitness saw a scuffle, but said it appeared McCarthy had Ortega under control. Both of the eyewitnesses said they turned away just seconds before the shooting began.

Even more troubling are the inconsistencies surrounding McCarthy’s gun. McCarthy told investigators that when he kicked Ortega to the ground, he must have knocked loose the backup revolver that he carried in an ankle holster. At some point during the officer’s struggle to handcuff Ortega, he noticed the revolver on the ground, just a couple feet from Ortega’s head.

Right after the shooting, while McCarthy was still at the scene, he told his supervisor that Ortega managed to grab the revolver and raise it towards him, according to initial statements by the supervisor, Sgt. Alan Karsh. (Karsh later said in a deposition that he was “foggy” about what McCarthy had told him.)

But a few hours after the incident, in his own interview with investigators, McCarthy said something different. He said that Ortega’s hand barely touched the revolver.

Ortega’s DNA wasn’t found on the backup weapon, though some traces couldn’t be matched to anyone. Neither Ortega’s nor McCarthy’s fingerprints were on the backup weapon.

After he pushed the revolver away during his struggle with Ortega, McCarthy told investigators that he got off Ortega and drew his primary gun. He said he’d barely unholstered it — only his right hand was on the pistol grip and his arm close to his side — when Ortega lunged at him, his hands coming within a foot of the gun, McCarthy said.

“What was your intent when you pulled [the gun] out? What was your thought process?” a homicide investigator asked McCarthy.

“My intent was hopefully he was going to run away,” McCarthy said, “and I [would be] able to grab my revolver … and resume pursuit of the suspect ….”

“What was your thought process when you switched from physical force to a deadly weapon? What was going through your mind?” McCarthy was asked.

“The guy’s trying to grab the gun. He wants to kill me,” he said. “And then when I saw him reaching for the pistol … he wants to grab that gun from me and he’s going to kill me with it.”

McCarthy said he gave Ortega no warning before firing twice, striking Ortega first in the abdomen, then, as he slouched over, in the back of the neck. The second shot traveled through Ortega’s spinal cord and pierced his heart.

After the second shot, McCarthy handcuffed Ortega and began performing CPR until other officers and paramedics arrived. Ortega was pronounced dead at 8:11 a.m.

The inconsistencies in McCarthy’s story were problematic for Burns, the judge in the lawsuit filed by Ortega’s widow. He noted them all in his November ruling that rejected the city’s attempt to toss the case.

Burns first had trouble with McCarthy’s account of what he did prior to pulling out his gun.

“McCarthy’s testimony has him completing the following actions with only two hands,” Burns wrote in his decision, “holding Ortega down, drawing a Taser with one hand, struggling to handcuff Ortega (presumably with his other hand), successfully cuffing Ortega’s one hand while Ortega’s other one got free, and moving to holster his Taser after seeing Ortega reach for the secondary weapon – somehow, McCarthy knocked the secondary weapon out of Ortega’s reach while one hand was restraining Ortega and the other was holstering a Taser.”

The city’s lawyers, who have appealed Burns’ ruling, said in a brief filed last week that the judge didn’t give enough credence to the totality of McCarthy’s statements about his attempts to handcuff and subdue Ortega before the killing. Indeed, the evidence shows that McCarthy described a more plausible sequence of events at one point during questioning by investigators.

Still, Burns found plenty more problems with McCarthy’s story. Take some of the forensic evidence.

McCarthy said Ortega’s hands were within a foot of the gun when it was fired. But there were no marks left by burning gunpowder on Ortega’s hands, clothing or wounds, which indicates that Ortega might not have been as close as McCarthy indicated he was.

Experts hired by Ortega’s widow questioned whether McCarthy and Ortega were level with each other when McCarthy fired, with Ortega moving to grab McCarthy’s service weapon. On the day of the shooting, McCarthy told investigators that both he and Ortega were rising to stand up. But the bullets’ steep trajectories suggest McCarthy was standing when he fired, while Ortega was on the ground and slightly bent forward, the experts said.

Then there are the issues with how the police department investigated the incident: No one did a walk-through re-enactment of the shooting with McCarthy, something even the city’s own expert said is recommended. And Frank Healy, the police department criminalist who wrote the crime-scene reconstruction report, said in a deposition that he never read the transcript of McCarthy’s interview with homicide investigators.

“Did you feel that [McCarthy’s] statement would be important to you for the purposes of preparing a reconstruction report?” asked Christina Denning, the attorney for Ortega’s widow.

“Yes,” Healy said.

Denning: “But you never reviewed the statement?”

Healy: “No.”

Denning asked Healy why such information would be important.

“Because part of my reconstruction report is to determine whether or not the statements made by the officer lined up with the evidence,” Healy said.

In their brief filed last week, the city’s lawyers argued that any inconsistencies in McCarthy’s story were immaterial and minor. Even if Ortega was further away from McCarthy than the officer indicated, he was still close enough to be a serious threat, the city said. That’s especially the case since the two had been in a struggle and McCarthy believed Ortega was going after his backup weapon. In short, the city’s lawyers argue, the totality of the evidence shows that McCarthy should receive the benefit of the doubt.

“The inconsistencies do not negate the fact that McCarthy had probable cause to believe he was in imminent serious physical harm and acted accordingly,” the brief said.

Both the San Diego Police Department and the City Attorney’s office declined comment for this story beyond the legal filing. A police spokesman did confirm that McCarthy remains an SDPD officer and is on active duty.

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Ten months after the shooting, District Attorney Bonnie Dumanis ruled that McCarthy’s killing of Ortega was justified. Relying mainly on McCarthy’s statement to investigators, Dumanis concluded that “Officer McCarthy fired at Mr. Ortega while attempting to arrest Ortega and in self-defense.”

In Dumanis’ report on the case, she didn’t note the many inconsistencies in McCarthy’s versions of what happened and the problems with the San Diego police department’s investigation. When asked whether the information that’s surfaced in the case would prompt a fresh look, a Dumanis spokesman said in a statement: “If new information regarding an officer-involved shooting comes to light after the District Attorney’s review is completed, it is possible that an incident could be re-reviewed.”

Shakina said Dumanis, whom she met with after the shooting, had promised her a thorough review, telling Shakina she would “treat this like Victor was her own son.”

“I want her to keep her promise,” Shakina said.