Police and FBI are questioning the suspected gunman in a shooting early Friday at a crowded midnight screening of the new Batman movie, “The Dark Knight Rises,” in Aurora, Colo., that left 12 people dead and 59 others wounded — the deadliest U.S. shooting since the Fort Hood massacre in 2009.

The suspect, identified by law enforcement officials as James Egan Holmes, 24, is in police custody. Aurora Police Chief Dan Oates said authorities are "confident" that Holmes — who was clad in all black clothing and wore body armor — acted alone and used an AR-15 assault rifle, a shotgun and a .40-caliber handgun in the attack. Another handgun was also found in his car, which was parked outside of the theater.

"We are confident that he acted alone," said Oates, adding that "many, many" rounds were fired.

Oates said Holmes' lone interaction with local police prior to the shooting occurred in October when he was cited for speeding.

Holmes is scheduled to make his initial court appearance on Monday at 8:30 a.m. local time in Centennial, Colo.

Earlier, police said Holmes’ apartment was booby trapped, leading authorities to evacuate five surrounding buildings. Oates said bomb technicians are determining how to disarm flammable or explosive material in the third-floor apartment. He says police could be there some time.

"We have an active and difficult scene there," he said.

Oates says pictures from inside the apartment are fairly disturbing, and the devices look to be sophisticated. FBI agents and police used a hook and ladder fire truck and put a camera at the end of 12-foot pole inside Holmes’ apartment, which is about four miles from the theater.

Police also have evacuated two research buildings at the University of Colorado Anschutz Medical Campus where the suspect in the Colorado shootings was a graduate student. A school law enforcement officials said it was a precaution, and there is no reason to believe staff or students are at risk.

KUSA-TV reports that Holmes kicked down an emergency door at the theater, threw in some type of a smoke bomb and began shooting when moviegoers started to run.

Authorities started to remove the bodies from the theater on Friday afternoon. Officials wheeled a black bag on a stretcher out of the front entrance, placing it in the back of a minivan. Ten people died in the theater, while two others died from their injuries later.

One sailor and two airmen were injured while at the theater, the Defense Department said, and another sailor known to have been at the theater was still unaccounted for.

The killings set off security concerns at theaters across the country, with local law enforcement weighing in on their own precautions.

New York City Police Commissioner Raymond Kelly said the NYPD is increasing security at movie theaters citywide.

"We're doing this to raise the comfort level," Kelly said. "We'd certainly encourage everybody to go about their business."

He also told reporters during a news conference that a contact in Colorado informed him that Holmes had painted his hair red and said he was “The Joker,” Batman’s nemesis who does not appear in the latest film.

Witnesses say they heard a series of explosions and up to 20 gunshots after the scene grew chaotic. About 100 witnesses were taken to a local high school to be questioned by police.

Police, ambulances and emergency crews swarmed on the theater after frantic 911 calls around 12:30 a.m. local time, officials said.

Holmes reportedly fired shots inside the theater and fled to the parking lot and was confronted by police already at the theater for crowd control. Holmes wore a bulletproof vest, police said, and was carrying a rifle and two handguns. The handguns may have been placed in the theater before the shooting.

The guns used in the attack were purchased at two separate Gander Mountain Guns shops, one in Thornton, Colo., and another in Aurora. The remaining guns were purchased at Bass Pro Shops in Denver, law enforcement sources told Fox News.

FBI spokesman Jason Pack said there's no indication in the investigation so far of any connection to terrorism.

President Obama said he is "shocked and saddened" by the mass shooting and urged the nation to "come together as one American family." He said his administration will do everything it can to support the people of Aurora, Colo. The White House says Obama, who was in Florida at the time of the shooting, was informed of the shooting by Homeland Security Adviser John Brennan.

"As we do when confronted by moments of darkness and challenge, we must now come together as one American family," Obama said in a statement. "All of us must have the people of Aurora in our thoughts and prayers as they confront the loss of family, friends, and neighbors."

Obama later spoke to supporters in Fort Myers, Fla., where he asked for a moment of silence.

“Everybody just take a moment," Obama said. "I hope all of you will keep the people of Aurora in your hearts and minds today. I am grateful to all of you."

Holmes attended Westview High School in San Diego, Calif., and graduated in 2006, the Poway Unified School District confirmed to Fox News.

Police released a written statement from Holmes' family: "Our hearts go out to those who were involved in this tragedy and to the families and friends of those involved."

James Wilburn was sitting in the second row of theater 9 after midnight when an emergency door opened and a man entered, the Denver Post reports.

"He was dressed in black," Wilburn told the newspaper. "Wearing a flack jacket and a gas mask."

The man was carrying a shotgun and had a rifle strapped to his back, Wilburn said. The gunman then dropped a canister, causing a noxious gas to spew out. He raised the shotgun and repeatedly fired toward the back of the theater.

Wilburn and three friends dove to the floor, hiding behind seats in front of them. The gunman was only five or six feet away, he said.

Once the shotgun was empty, the gunman calmly dropped it to the floor, took the rifle and went on firing. Wilburn heard roughly 30 shots, the Denver Post reports.

Meanwhile, 21-year-old Naya Thompson and her 22-year-old boyfriend Derrick Poage were running for their lives. Thompson said the gas spread and the gunman may have dropped two canisters.

"It was like a tear gas," Thompson told the newspaper. "I was coughing and choking and I couldn't breathe."

James Cameron, who was in an adjacent theater, said he heard commotion and screaming. People seated around him began coughing and having difficulty breathing.

"By the sound of it, it sounds like there could have been three or four guys shooting," he said.

Oates said there's no evidence of any other attackers. There was also no immediate word of any motive.

Bejamin Fernandez, 30, told the Denver Post that he heard a series of explosions. He said that people ran from the theater and there were gunshots as police shouted "get down!"

Fernandez said he saw people falling, including one young girl.

Jordan told the paper that one girl was struck in cheek, others in stomach including a girl who looked to be around 9-years-old.

Jordan said it sounded like firecrackers until someone began yelling, "They're shooting out here!"

Hayden Miller told KUSA-TV that he heard several shots.

"Like little explosions going on and shortly after that we heard people screaming," he told the station.

Hayden said at first he thought it was part of a louder movie next door. But then he saw "people hunched over leaving theater."

Some moviegoers said they thought the attack was part of the show. Then they saw a silhouette of a person in the smoke at the front of the theater, pointing a gun at the crowd.

"I told my friend, `We've got to get out of here,' but then he shot people trying to go out the exits," Jennifer Seeger told NBC's "Today." She the shooter made his way up the aisle, shooting as he went, saying nothing.

The youngest victim reported was a 6-year-old being treated at Children's Hospital Colorado, where a total of six victims were taken. Their condition wasn't known.

Two people in critical condition were rushed to nearby Swedish Medical Center, spokeswoman Nicole Williams said.

Aurora is on Denver's east side and is Colorado's third-largest city with 327,000 residents. It is home to a large Defense Department satellite intelligence operation at Buckley Air Force Base, as well as The Children's Hospital, the University of Colorado Hospital and a future Veterans Affairs hospital.

The incident was the worst mass shooting in the U.S. since the Nov. 5, 2009, attack at Fort Hood, Texas. An Army psychiatrist was charged with killing 13 soldiers and civilians and wounding more than two dozen others.

In Colorado, it was the deadliest since the Columbine High School massacre on April 20, 1999, when two students opened fire in the Denver suburb of Littleton, killing 12 classmates and a teacher and wounding 26 others before killing themselves. Columbine High is about 12 miles from the theater.

Fox News' Jennifer Griffin, FoxNews.com's Joshua Rhett Miller and The Associated Press contributed to this report.

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