Oct. 6, 2009 -- When Tony Arambula managed to corner an armed intruder in his son's bedroom he expected police to come to his aid.

Instead, a Phoenix police officer confused Arambula for the intruder and shot him six times before realizing his mistake, a moment captured on the 911 call with a simple "F**k."

Even after realizing their mistake, Arambula said he was treated roughly, being dragged out of the house and transported briefly on the hood of a police car.

Now Arambula, 35, who survived but faces a lifetime of pain, is suing the city of Phoenix and the officers who responded to his house that night.

The lawsuit, filed in Maricopa County Court, alleges that Phoenix Police Officer Brian Lilly and his on-scene supervisor, Sgt. Sean Coutts, quickly conspired to cover up the mistake, not realizing that 911 was still recording Arambula's call for help.

CLICK HERE to listen to Tony Arambula's 911 call to Phoenix police.

Lillly has been cleared of any wrong doing by the Phoenix Use of Force Board, but the Arambulas are suing the officer, Coutts, the city of Phoenix, the Phoenix police department and a number of unidentified emergency workers for at least $5.75 million.

"It's clearly unfortunate," said Officer Mark Spencer, president of the Phoenix Law Enforcement Association which represents 2,600 officers. "Our officers feel terrible this occured."

But, Spencer told ABCNews.com, PLEA also disputes some of the Arambulas' account, including that the father of two was shot in the back.

"Clearly where the blame lies is with the bad guy," Spencer said, adding that the intruder put "everyone at risk."

As for Arambula's actions that night, Spencer said, "I don't think he did anything wrong."

He added, "We agreed with the board's decision that the officer's response and action was reasonable within police policy."

The city of Phoenix did not immediately respond to a request for comment.

According to the lawsuit, Arambula, his wife Lesley and their two sons were at home on Sept. 17, 2008, when they heard two gunshots outside shortly before an intruder crashed through their front window and pointed a 9mm gun at Arambula and 2-year-old Zachary.

The gunman, according to the lawsuit, then took off down the hall into 12-year-old Matthew's bedroom. Arambula, who had sent his wife and toddler outside the house, retreived his own handgun and cornered the intruder who was shouting that "someone was after him and going to get him."

After calling for Matthew, who had been hiding in his closet, and sending the boy outside, Arambula called 911 while continuing to point the gun at the intruder. Lesley Arambula also placed a call to 911 within seconds.

'You Killed the Homeowner'

Officers had already been in the neighborhood responding to an earlier call about a "Hispanic male" who had threatened a woman at a nearby house. According to the lawsuit, Lesley Arambula flagged them down and yelled for help.

The lawsuit alleges that Lesley Arambula told Coutts, a 12-year-verteran of the Phoenix Police Department, that her husband was alone in the house with the intruder at gunpoint, but that Coutts never gave the information to Officers Lilly and Dzenan Ahmetovic, who had entered the house.

Spencer confirmed that Coutts never relayed to the officers that Arambula was holding the intruder at gunpoint.

What happened next is in dispute. The lawsuit claims that Arambula had his back to the officers when Lilly opened fire without warning, hitting Arambula six times. The last two shots allegedly hit Arambula when he was on the ground.

Spencer told ABCNews.com that the officers reacted only with the information they had at the time, without the benefit of hindsight.

According to a transcript of the 911 call attached to the lawsuit, Arambula told the dispatcher, "I'm the homeowner. You just killed, you killed the homeowner. The bad guy's in here."

About two minutes into the call, Arambula was recording saying goodbye to his family, saying "I love you ... I love you."

About three minutes later, with the 911 call still recording, an officer was picked up saying "We f**cked up," and then Lilly saying, "I f**cking shot this guy ... f**cked up."

About six minutes into the call, Coutts was recorded as saying "Was the gun down here?" Lilly's response was recorded as "I don't know. I heard screaming and I (inaudible) fire."

"Don't worry about it," Coutts was recorded as saying. "I got your back."

But Spencer, who denied any attempt at a cover up, told ABCNews.com that it was his understanding that Arambula was facing the officers while holding his gun, contradicting Arambula's claim that his back was to the officer.

While PLEA argued that Arambula was not shot in the back, Arambula's attorney Michael Manning told ABCNews.com that Arambula's surgical doctor determined that the first bullet entered through his back and came out his abdomen.

According to the lawsuit, Arambula was eventually dragged out of the home, which PLEA Officer Jerry Gannon said was done for his safety because police did not know whether an intruder may have still been in the house.

But the lawsuit alleges further mistreatment even after the intruder was taken into custody, including that Arambula was dragged from the patio to the gravel in front of the house, his head banged against a post on the fence.

Police Error Could Mean Amputation for Homeowner

The lawsuit claims Arambula, who had still not received medical attention, was picked up again and placed on the hood of a hot squad car and driven for a time down the street before being transferred by ambulance to a hospital where he immediately underwent surgery.

Lesley Arambula, the lawsuit claims, was interrogated for hours and kept in a squad car with her children with no word on her husband's condition.

At the hospital, Arambula was questioned by detectives immediately after coming out of surgery and told, according to the lawsuit, that the intruder would be cited and released because he was found to be unarmed.

"Tony was incredulous at their conclusion and asked the police if they had looked under Matthew's bed. The police assured him that they had done so and completed a thorough investigation, but promised to go back and look again," the lawsuit stated.

The intruder's gun was found under the boy's bed during a subsquent search.

According to the lawsuit and Manning, Arambula's wrist was so badly damaged in the shooting that he faces more surgery and possibly even amputation. Even if he keeps the wrist, the lawsuit alleged, he may suffer some permanent loss of the use of his hand and wrist.

Doctors have already intentionally broken Arambula's right hip to collect bone fragments for use in his wrist.

"Even if Tony gains back full use of his wrist, doctors have told him to expect a lifetime of pain and arthritis as a result of his wounds," the lawsuit stated. "The bullets that penetrated Tony's knee and leg have left him with daily pain and swelling."

And, the lawsuit claims, the damage is more than just physical.

Lesley Arambula was forced to take time off work and was recently laid off. The boys are in therapy and the family has had to pay thousands of dollars in repairs to their home to clean the bloody carpet and walls and fix the bullet holes.

Arambula was even mistakenly threatened with arrest when he went to the police station months afterward to pick up his handgun and other items seized by police as evidence.

Arambula was eventually let go after convincing police that two outstanding felony drug warrants in his name were incorrect and that he had been at home in Arizona recovering from the shooting when the warrants were issued, not in Washington state and Oregon.

"But, they warned him to 'be careful' suggesting that he might just be arrested and taken to jail if he encountered any police, because of the 'confusion' regarding the warrants," the lawsuit stated.

Though the notice of claim filed with the defendants in advance of the lawsuit says the Arambulas are asking for $5.75 million, Manning noted that the cost could go higher once they go before a jury, especially if Arambula's medical costs skyrocket from the amputation of his wrist.

Spencer confirmed to ABCNews.com that other than the mandatory three days paid leave after the shooting, Lilly has remained on the job in full capacity. Neither he nor Coutts were disciplined.