MALONE –– Approximately 16 miles from where his partner was killed, with 1½ miles to go before making it across the Canadian border, escaped cop-killer David Sweat was subdued Sunday afternoon by state police after taking two bullets that brought him down, leaving him in critical condition.

And with the close of what had been more than three weeks of hunting down Sweat and fellow murderer Richard Matt, a new investigation begins: one into the Clinton Correctional Facility in Dannemora, Gov. Andrew M. Cuomo said Sunday night during a news conference from the ski lodge at Titus Mountain.

“As I’m sure you’ve heard already, the nightmare is finally over,” Cuomo said to the crowd gathered at the ski lodge.

“This is the first escape in over 100 years, but one escape is one escape too many,” Cuomo said. “We will have an ongoing investigation to find out who was involved. ... We will also be conducting an investigation into the systems in that prison and how could this happen.”

An investigation is already underway into the prison by state Inspector General Catherine Leahy Scott, Cuomo said.

For the second time in almost 48 hours, Cuomo and state police Superintendent Joseph A. D’Amico approached a crowd of cheering community members at the announcement of the capture of a murderer who escaped from the prison June 6.

“It took 22 days, but we can now confirm as of two days ago, Mr. Matt is deceased and the other escapee, Mr. Sweat, is in custody,” he said.

Sweat, 35, was serving a life sentence without parole for killing a sheriff’s deputy near Binghamton on July 4, 2002. Matt, 49, of the Buffalo area, was doing 25 years to life for the 1997 kidnapping, torture and hacksaw dismemberment of his former boss.

Matt was shot and killed Friday, near the Duane town border, by a U.S. Customs and Border Protection agent after authorities tracked him down in the woods near a cabin he had broken into near Fayette Road in the town of Malone.

About 3:15 p.m. Sunday, police called for assistance at Coveytown Road, reporting “suspect shot, in custody” in the hamlet of Constable, after Sweat was seen jogging on the roadside by state police Sgt. Jay Cook while he was on patrol. Cook called to Sweat, who then took off across a field, heading for a treeline, D’Amico said.

“At some point, while running across a field, he realized that Sweat was going to make it to a treeline and possibly could have disappeared and he fired two shots from his handgun, hitting Sweat twice in the torso,” D’Amico said.

Sweat was treated by Constable Volunteer Rescue Squad at the scene and was taken to Alice Hyde Medical Center in Malone, where he was listed as stable. He then was flown to Albany Medical Center, a trauma center, where officials said his condition was downgraded to critical Sunday night.

“We couldn’t be happier that we were able to apprehend him and not lose him,” D’Amico said. “It has been a long three weeks.”

Melanie Clookey, who lives on Poplar Road near where Sweat was captured, said she was driving down the road at 3:13 Sunday afternoon when she came across a state police patrol car stopped diagonally on the road with its driver’s door open and no one in sight. As she drove past, a second patrol car rushed up.

The activity convinced her the scene was unsafe, and she drove quickly away, said Clookey, who was certain of the time because she had just made a telephone call.

The Constable emergency squad was dispatched to the scene at 3:15 p.m.

“I was lucky that I wasn’t a few minutes early,” Clookey said.

Authorities tracked down more than 2,300 leads with the use of more than 1,300 men and women trudging through dense woods, swamps and fields, D’Amico said.

During the investigation into the shooting death of Matt, D’Amico said, police obtained Sweat’s DNA from discarded material.

“It was picnic-style pepper shakers, and we believe that possibly these two males were using pepper to throw the scent off of the dogs who were tracking,” D’Amico said. “We did have difficulty tracking, so it was fairly effective in that respect.”

An autopsy was conducted Saturday on the remains of Matt at Albany Medical Center by Dr. Michael Sikirica.

Matt’s cause of death was determined to be severe skull fractures and brain injuries due to gunshot wounds to the head.

An examination of the body revealed bug bites on the lower extremities, blisters and minor scrapes –– all consistent with living in the woods for three weeks, police said.

A preliminary investigation revealed a U.S. Customs and Border Protection Tactical Unit member discharged several rounds from a semiautomatic weapon, striking Matt in the head three times.

Toxicology results are pending.

Assemblywoman Janet L. Duprey, R-Peru, said of the newly announced investigation into Clinton Correctional Facility that it is unfortunate the escape happened with Superintendent Steven Racette in charge of the maximum-security prison.

“He is one of the best in the state. It is so unfortunate that this happened on his watch, because the guy knows corrections. He is great,” Duprey said. “I hope no quick judgments are made about those corrections officers. I looked them in the eye and they were exhausted. They are determined, and the happiest place right now in the north country is at Clinton Correctional Facility and all the men and women who worked there because they wanted this over.”

But Duprey said whoever helped in the escape will “have the book thrown at them.”

Two prison employees –– civilian tailor shop instructor Joyce Mitchell and corrections officer Gene Palmer –– have been charged so far in connection with the escape of Matt and Sweat.

“As somebody who serves in the Assembly, I know what it is like to be painted with the same brush, and the vast majority of those corrections officers and civilian employees are outstanding state employees and they do a great job day in and day out,” Duprey said. “It will be a lot easier to go over and boost their spirits tomorrow, won’t it?”

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