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.
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.