Chris Bollwage, mayor of Elizabeth, N.J., told reporters that Rahami — whose last known address was in that city — had been taken into custody Monday in the neighboring city of Linden. Two police officers were shot during the encounter, according to authorities, one of them struck in their protective vest.

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Rahami — a naturalized U.S. citizen born in Afghanistan, according to the FBI — was also shot and was taken away in an ambulance, officials said.

Television footage showed the suspect being wheeled into an ambulance, hands cuffed, eyes open. He was taken to University Hospital in Newark, according to a hospital spokeswoman, but his condition was not immediately available.

Rahami was charged Monday with five counts of attempted murder of a law enforcement officer related to the gun battle in Linden, said acting Union County Prosecutor Grace H. Park. He has also been charged with two second-degree counts related to his possession of a handgun.

After the gunfire ended in Linden, Rahami — who was shot multiple times — was taken to University Hospital in Newark for surgery, officials said. They did not elaborate on his condition after surgery. Bail for Rahami has been set at $5.2 million by a state superior court judge.

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Police and the FBI had announced early Monday that they were seeking Rahami in connection with the bombings in New Jersey and Manhattan’s Chelsea district, though his role in the incidents remains unclear.

“We have every reason to believe this was an act of terror,” New York Mayor Bill de Blasio (D) said at a news conference Monday afternoon discussing the bombings and Rahami’s arrest. Earlier in the day, he had said the investigation was leaning in that direction.

Authorities are not seeking any other individuals at this time, de Blasio said.

Now that Rahami is in custody, the investigation is shifting to focus on whether he acted alone and what his motivation may have been, said James O’Neill, the New York police commissioner.

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William Sweeney Jr., assistant director in charge of the FBI’s New York division, said that authorities have found “no indication that there is a [terror] cell operating in the area.”

A federal law enforcement official said Monday that federal terrorism charges against Rahami are expected, adding that such charges are likely in both New York and New Jersey. In addition, Rahami is also expected to face criminal charges stemming from the gun battle leading to his capture.

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Preet Bharara, U.S. Attorney for the Southern District of New York, said during the news conference Monday that his office and possibly its counterpart in New Jersey “will be working to put together as comprehensive and thorough a collection of allegations as makes sense.”

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Another law enforcement official said that police had footage almost immediately after the explosion on Saturday in New York, along with “a number of different pieces of physical evidence” including fingerprints and DNA, though the official would not elaborate on which proved key in the investigation.

So far, the official said there is no information there are any additional devices remaining. As of Monday evening, it appeared Rahami had not spoken to investigators, the official said.

The manhunt for Rahami came after authorities took five people into custody Sunday night for questioning in connection with the Chelsea bombing — not long before law enforcement in New Jersey worked to render safe “multiple improvised explosive devices” discovered at a train station Sunday in Elizabeth, just across from Staten Island.

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Federal law enforcement officials have told The Washington Post they believe all three cases involving explosives in New York and New Jersey to be linked. They would not say whether the five people taken into custody Sunday night and later released were linked to Rahami or how Rahami’s family fit in, if at all.

The developments sowed further concern about terrorism in the region and across the country. Already, police had been investigating three weekend incidents — including a stabbing attack in a Minnesota mall — that took place within a 12-hour period Saturday.

The investigation into the bombings has drawn in all levels of law enforcement and intelligence, and an increasing number of local, state and national officials have condemned the incidents as acts of terrorism.

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“It’s been an extremely busy two days, obviously,” said O’Neill, the New York police commissioner, who assumed the post on Saturday.

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Law enforcement officials said they were investigating whether Rahami could have been influenced by international militant groups or the ongoing conflict in his homeland, though they have not specified whether he operated as a lone wolf or has deeper connections to international terrorist groups.

Rahami was born in Afghanistan, the FBI said. On Monday, Hamdullah Mohib, Afghanistan’s ambassador to the U.S., said his government strongly condemned the bombings.

“We stand ready and willing to help with this matter if U.S. authorities request our cooperation,” Mohib said in a statement. “Afghanistan and its people desire peace above all else, and stand in solidarity with Americans against all forms of hatred and violence.”

Authorities were able to pull fingerprints from the Manhattan bomb that did not detonate, according to Rep. Peter King (R-N.Y.), who said he was briefed on details of the attack and shown the Chelsea bombing site by the FBI the morning after the explosion.

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King said that investigators connected the bombs in New Jersey and in New York due to “similarities” in the explosives, among other things, and said that authorities used a cellphone attacked to the bomb that did not explode and traced it to another cellphone.

Still, King said that even though the bomb was made by an apparent amateur, it appeared to be impressive. He said it’s a matter of luck that more people were not seriously hurt.

“The dumpster that was exploded was thrown down the street,” King, a member of the House Homeland Security Committee, said in an interview. “It was sent flying. You had ball bearings everywhere. If streets had been crowded, there would have been bad injuries. There were windows broken as high as the third floor. It did quite a bit of damage.”

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King said that he has been told that Rahami’s “trips to Afghanistan changed him,” adding that the 28-year-old had also visited Pakistan at some point.

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After Rahami was arrested Monday, details began to emerge about how authorities found him.

Linden Police Capt. James Sarnicki told a local NBC affiliate that officers responded Monday to a call about a person sleeping in the doorway of a local bar. When police approached the man, they noticed his resemblance to the images on the wanted bulletin for Rahami.

Police then ordered him to show his hands, Sarnicki said, and Rahami “pulled out a handgun and fired one shot at the officer, striking him in the abdomen. Fortunately, the officer had a bulletproof vest on, which sustained most of the round.” That officer returned fire, the police captain said, but Rahami walked away.

“I understand that the suspect was indiscriminately firing his weapon at passing vehicles,” Sarnicki said. Rahami was eventually shot by police “more than once and … taken down to the ground,” Sarnicki said.

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During the exchange of gunfire, Linden Mayor Derek Armstead said, a bullet ricocheted off a police vehicle and grazed another officer. A third officer was treated for high blood pressure.

“All three are going to be fine,” the mayor said. “We’re grateful no one was hurt.”

A Linden resident who went to the scene of the arrest said he saw the suspect lying on the ground on his side, handcuffed and seemingly in pain. Within 10 minutes, more than 100 law enforcement officials swarmed the area, said the witness, who did not want his name used.

The two wounded officers were loaded onto ambulances and taken away first, and another ambulance took Rahami away 10 to 15 minutes later, the man said.

President Obama spoke on the phone Monday with the two officers who were injured, according to the White House. He also spoke with an off-duty officer who shot and killed a man attacking people inside a Minnesota mall on Saturday, thanking all three officers for their actions in recent days.

Before the shootout in New Jersey involving the two officers, FBI agents had also launched an “operation” at an address on Elmora Avenue in Elizabeth, about a mile away from New Jersey Transit’s Elizabeth station. Court records show members of the Rahami family live and work at the address, where a restaurant called First American Fried Chicken is on the ground floor.

Court records show that several members of the Rahami family had owned and operated the restaurant since 2002. It is unclear when Ahmad Rahami himself lived there or what role — if any — he had in the business.

In 2011, the Rahami family sued the city of Elizabeth and several police officers, alleging they had been inappropriately cited for keeping their business open past 10 p.m. and harassed by police.

They alleged that a man in the neighborhood told them “you are Muslims” and “Muslims make too much trouble in this country” and complained unfairly to law enforcement, who singled them out “solely on animus against [their] religion, creed, race and national origin.”

In one instance, they alleged, two Rahami family members were arrested for attempting to record a conversation with officers.

New York Gov. Andrew Cuomo (D) told CBS News on Monday that “there may be a foreign connection” involving the bombing in Manhattan, though he did not elaborate.

About 8:45 p.m. Sunday, the FBI and the New York Police Department stopped what the bureau’s New York field office called a “vehicle of interest” in the Manhattan bombing investigation and took five people into custody.

On Monday afternoon, authorities said that the passengers in the car had been questioned by Joint Terrorism Task Force agents and detectives, but said they were not in custody and none had been arrested.

Law enforcement also combed an area around the train station in Elizabeth, where a backpack with “multiple improvised explosive devices” was found.

Bollwage, the Elizabeth mayor, said that up to five devices were discovered inside a backpack, and one of the devices — found around 8:30 p.m. Sunday — exploded as it was being disarmed shortly after 12:30 a.m. Monday. The New Jersey Transit rail system halted rail service near Newark Airport due to the police activity. Regular service was restored before dawn.

The mayor said Monday that two homeless men found the explosives. Thinking there would be something valuable in the backpack, they opened it — but found what appeared to be explosive devices and reported it to the police.

They were “on the side of the angels,” Bollwage said, noting that the men didn’t get blown up when they touched the bag. If the bombs had exploded hours later, during rush hour, “hundreds of people would have been killed and injured,” the mayor said.

Each of the weekend incidents — the discovery of the devices in Elizabeth, the bombing that injured 29 in Chelsea, an explosion along the route of a scheduled race in Seaside Park, N.J., and a stabbing that wounded nine in a St. Cloud, Minn., mall — raised the possibility of terrorist connections, prompting federal and local law enforcement to pour major resources into determining exactly what happened and why.

A news agency linked to the Islamic State claimed Sunday that the suspect in Minnesota, who was fatally shot by an off-duty police officer, was “a soldier” of the militant group, though there was no confirmation of what connection the man may have had with the terrorist group.

A claim of responsibility is no guarantee that the terrorist group directed or even inspired the attack, and authorities said they were still exploring a precise motive. The Islamic State made no similar claims about the New York and New Jersey incidents.

In New York, authorities said there was no evidence that the mysterious Saturday-night explosion was motivated by international terrorism, though they confirmed that the bombing was intentional. “This is the nightmare scenario,” Cuomo said.

Earlier Sunday, New York’s governor said nearly 1,000 police officers and National Guard troops would be sent to bus stops, train stations and airports, as investigators with the New York Police Department, the FBI and the Bureau of Alcohol, Tobacco, Firearms and Explosives worked to identify the person or people responsible for the explosion.

One law enforcement official said that while it was looking like the New Jersey and New York blasts “might be connected,” investigators still didn’t have any hard evidence. The official also said that only one of the three pipe bombs in New Jersey detonated.

Those injured in the Saturday night blast in Chelsea had been released from hospitals by Sunday.

The Manhattan explosion occurred about 8:30 p.m. Saturday in the area of West 23rd Street between Sixth and Seventh avenues, injuring 29 people as it hurled glass and debris into the air, officials said. Surveillance video showed passersby running to get away from the blast, and investigators said they would comb through that and older footage to try to identify those responsible.

Authorities said the explosion was produced by some type of bomb, and they posted on Twitter a photo of what appeared to be a mangled Dumpster or garbage container. Masum Chaudry, who manages a Domino’s Pizza near the scene, said the explosion “shook the whole building” and caused “total chaos.”

Investigators are somewhat puzzled by the placement of the bomb, which appeared to mitigate the impact of the blasts. “There’s some unanswered questions on that,” said one federal law enforcement official. “Why there? Some of that from our point of view isn’t adding up.”

Said Cuomo: “When you see the amount of damage, we really were very lucky there were no fatalities.”

A short time after the explosion, just a few blocks away, police found another potentially explosive device, which looked like a pressure cooker with wiring, according to a law enforcement official who spoke on the condition of anonymity to discuss the ongoing investigation. Pressure cookers were used in the two bombs detonated at the Boston Marathon in 2013.

The New York police said that this pressure-cooker-type device was first rendered safe at a Bronx facility. This device and materials from Seaside Park, N.J., were sent to the FBI’s lab in Quantico, Va., where they and the remnants of the device that exploded will be analyzed, authorities said.

Officials differed on whether to call the Saturday night explosion an act of terrorism. Cuomo said: “It depends on your definition of terrorism. A bomb exploding in New York is obviously an act of terrorism, but it’s not linked to international terrorism.” Over the weekend, city, police and FBI officials said it was too early to determine any type of motivation, though they insisted they would not shy from labeling the crime an act of terror if it became appropriate to do so.

The incidents came as foreign leaders, including many heads of state, were heading to Manhattan for the United Nations General Assembly. Secretary of State John F. Kerry arrived Saturday, while President Obama arrived in the city Monday.

The annual U.N. meeting — held more than two miles from the site of the explosion in Chelsea — is traditionally a challenging time for New York, as many roads are shut down and the heavy security leads to traffic jams. Officials said they had already prepared to beef up security, and now they would intensify those efforts.

Speaking in New York, Obama said there was no known connection between the stabbings in Minnesota and the incidents in New York and New Jersey. But the attacks only reinforced his resolve to continue fighting the Islamic State, both on the ground and online, he said.

“We will continue to lead the global coalition in the fight to destroy ISIL, which is instigating a lot of people over the Internet to carry out attacks,” Obama said, using one of the acronyms for the Islamic State. “We’re going to continue to enlist tech companies and community and religious leaders to push back against online extremist content and all messages of hate.”

The president also emphasized the need to be vigilant but cautioned citizens against giving in to fear.

“At moments like this, I think it’s important to remember what terrorists and violent extremists are trying to do: They are trying to hurt innocent people, but they also want to inspire fear in all of us and to disrupt the way we live and to undermine our values,” he said.

On the campaign trail, the Democratic and Republican presidential candidates offered varied reactions to news of the incidents.

“I think this is something that will maybe get — will happen perhaps more and more all over the country,” Donald Trump told “Fox and Friends.” “It’s a mess and it’s a shame, and we’re going to have to be very tough.”

Trump also said he agreed with early reports of a possible foreign connection to the bombings, and argued that the stricter immigration policies he has proposed would better protect the U.S. from terror.

Speaking in White Plains, N.Y., Clinton told reporters that the United States should launch an “intelligence surge” to identify and thwart attacks before they are carried out.

“This threat is real, but so is our resolve,” she said. “Americans will not cower. We will prevail. We will defend our country. A lot of the rhetoric from Donald Trump has been seized on by terrorists, particularly ISIS. They want to use that to recruit more fighters to their cause by turning it into a religious conflict. That’s why I’ve been very clear. We’re going after the bad guys and we’re going to get them, but we’re not going after an entire religion.”

Speaking at a town hall event Monday, New Jersey Gov. Chris Christie (R) said there “is no doubt in my mind that the incidents in New York, Elizabeth and Seaside Park are connected.” Though officials haven’t determined a motive in the attacks, Christie mentioned Muslim terrorists in his remarks.

“Those who are radical, especially radical Islamic terrorists, need to be called out,” he said. “We don’t know what the motivation is for the last 48 hours, but I think we have feeling for what it is.”

The Council on American-Islamic Relations, a Washington-based advocacy group, said Monday that it welcomed Rahami’s arrest.

“American Muslims, like all Americans, reject extremism and violence, and seek a safe and secure nation,” CAIR’s Executive Director Nihad Awad said in a statement. “Our nation is most secure when we remain united and reject the fear-mongering and guilt by association often utilized following such attacks. We stand together with our fellow Americans in New York, New Jersey and Minnesota as we deal with the troubling phenomenon of domestic terrorism.”

The Chelsea explosion occurred about 11 hours after a pipe bomb exploded in a Jersey Shore garbage can, shortly before a scheduled charity 5K race to benefit Marines and Navy sailors. No one was hurt.

Officials said that device, too, would be sent to the FBI lab in Quantico, though Cuomo noted the pipe bombs used in New Jersey “appear to be different” than those in New York.

Two law enforcement officials said residue of tannerite — used primarily for making exploding targets for firearms practice — was found in material that had detonated in New York. The explosive material found in New Jersey was a black powder. The two officials said a cellphone was used to detonate the explosives in both New York and Seaside Park, N.J. Bollwage said there was no cellphone with the devices in Elizabeth.

Nakashima reported from New York, Zapotosky, Wang and Berman from Washington. Sarah Larimer in New Jersey, Philip Bump in New York and Brian Murphy, Kristine Guerra, Sari Horwitz, Sean Sullivan, Steven Overly, John Wagner, Julie Tate, William Wan, Derek Hawkins and Cleve R. Wootson Jr. contributed to this report, which has been updated multiple times since it was first published Sunday night.