Mateen appeared through a hole that was blown open by the bomb squad, and officers opened fire, said Orlando police Capt. Mark Canty.
It's not clear who fired first, or how many shots there were. It is still unknown if any of the hostages were struck by any friendly fire, Canty said.
Officers blew the first hole in the wall between the two bathrooms at about 5:02 a.m. Officers then opened a second hole that was to a bathroom stall, but no one could get out.
Hostages started streaming out of the third hole, Canty said. There were five breaches in all.
After most of the hostages got out, Mateen emerged from the first hole around 5:14 a.m.
There was a barrage of shots and Mateen was taken down in that hallway.
Ten Orlando police SWAT team members and three Orange County deputies fired.
Canty talked about SWAT protocols, training and tactics in the response to the massacre where 49 people were killed and more than 50 wounded.
In active-shooter situations, officers are trained to go toward the gunfire and engage the shooter.
That's what Officer Adam Gruler did when he heard shots from the parking lot around 2:02 a.m. June 12, Canty said. He fired at Mateen from the outside.
"That is what we want to happen," said Canty.
Officers waited until 2:08 a.m. to go inside.
"It's not a matter of just jumping out of your car and running into the building," Canty said. "You have to find a way to enter the building."
Six officers — five with SWAT training — broke a large glass window on the south side of the club, Canty said.
Officers shot at Mateen about 2:18 a.m., and he then barricaded into a bathroom. Orlando police has maintained there were no shots fired after that until the final gun battle about three hours later. But witnesses and a dispatch records released Thursday by the Orange County Sheriff's Office say there was shooting after 2:30 a.m. It's unknown who fired those rounds.
Either way, Orlando police started treating Mateen as a barricaded gunman when he went into the bathroom. That's when there was a "full call-out" and more than 35 SWAT team members responded, Canty said.
"When there's no more shooting, you need slow down [and] assess," he said. "You want to be a little more methodical. You don't just want to rush into a situation where he has hostages because you don't know what he has. You don't know the layout of the bathroom. You don't know what he is capable of."
Throughout the ordeal, officers rescued "dozens and dozens of people," from other parts of the club, Orlando police spokeswoman Michelle Guido said.
Mateen had three conversations with crisis negotiators between 3 and 16 minutes long where he pledged allegiance to the Islamic State.
He told a dispatcher at 4:29 a.m. that he was going to blow up hostages with bomb vests within 15 minutes. Police breached the wall at around 5:02 a.m. No bombs were found.
There has been questions as to why police didn't decide to breach the wall sooner.
"The goal is to try to rescue as many people as you can," he said. "It does take time to be able to do [an explosive breach]. It's not something that's immediate. From the beginning of this we were moving and doing things to get as many people out alive as we could."
Canty said as more information comes to light, the department can do an assessment of what it did well and what it could improve upon.
He called the actions of the officers heroic.
"Forty-nine people lost their lives, and that is terrible and that is tragic," he said. "But there's a lot of people that survived because of the actions of those officers and medical personal that responded."
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