The FBI invokes the "public safety exception" with Boston bombings suspect Dzhokhar Tsarnaev. Chris Hayes breaks down what this means.

The arrest of Dzhokhar Tsarnaev ended the manhunt for the Boston Marathon bombers, but it set in motion an equally intense phase of the case that will begin with the grilling of the man who – for now at least – is the only surviving suspect.

An indication of the complex investigation ahead came Friday night, when an Obama administration official told NBC News that Tsarnaev would not be given a Miranda warning when he is physically able to be interrogated after receiving medical treatment.

Instead, the official said, the government will invoke a legal rule known as the "public safety exception," which will enable investigators to question Tsarnaev without first advising him of his right to remain silent and to be afforded legal counsel.

The exemption can be invoked when information is needed to protect public safety. In this instance, the government believes it's vital to find out if Tsarnaev planted any other explosives before his capture or whether others might have plotted with him to do so, said the official, speaking on condition of anonymity.

While the crisis is over, the investigation of what motivated the suspects is just beginning. NBC's Michael Isikoff reports.

Tsarnaev’s older brother, Tamerlan, was killed in a shootout with police early Friday, and it was not clear until late Friday that authorities would be able to question their remaining prime suspect.

Until shortly before his capture around 8:45 p.m. ET, the wounded and bleeding Tsarnaev exchanged gunfire with authorities in Watertown, Mass., while sheltering in a plastic-wrapped pleasure boat.

Officers on the scene and the brass in the command center were both clearly elated by the outcome.

“We always want to take someone alive so we can find out what happened,” Boston Police Commissioner Ed Davis said at a media briefing an hour later, “and we can hold them to justice."

High Value Detainee Interrogation Group

The rule waiving the Miranda warning does not set a precise limit on how long a suspect can be interrogated before being advised of his rights, but it likely buys authorities no more than 48 hours.

Richard Engel, NBC News chief foreign correspondent, talks with Rachel Maddow about the likely interrogation of Marathon bombing suspects Dzhokhar Tsarnaev, and how the public celebration of the law enforcement victory in this case undermines what would have been a bragging point for recruiters of terrorists worldwide.

During that time Tsarnaev, 19, will be questioned by a federal government team called the High Value Detainee Interrogation Group, consisting of officials of the FBI, CIA and Defense Department. Though he will not have a lawyer present, any statements he makes during the questioning will be admissible in court.

Among the questions investigators are certain to focus on is whether he and his brother had help in plotting or carrying out the terrorist attack at the finish line of the marathon. The dual blasts from pressure cookers packed with explosives and shrapnel killed three people and injured 176.

That question took on more urgency when police in New Bedford, Mass., south of Boston, announced Friday evening that three people there had been taken into custody as part of the bombing investigation.

In addition to possible co-conspirators in the U.S., the interrogators also will want to know whether the brothers, both ethnic Chechens, received any assistance from overseas.

Travel records obtained by NBC New York showed that Tamerlan Tsarnaev left the country for six months in 2012, flying to Moscow on Jan. 12 and returning on July 17. Where he went and what he did after his arrival in Russia could expand what so far has been a domestic manhunt into a global one.

Enemy combatant?

Suspicions that the elder brother could have received terrorist training or support abroad were heightened Friday, when an official familiar with the matter told NBC News that a foreign government had expressed concern in 2011 that Tamerlan Tsarnaev could have ties to terrorism. The official said the FBI investigated, but found no such links and reported the findings back to the foreign government.

Even if authorities determine that the Tsarnaevs received support from an overseas terrorist organization, the Obama administration official said the government will not seek to declare him an enemy combatant and try him before a military commission, as it has done with senior al Qaeda officials captured overseas and imprisoned at the Guantanamo Bay detention camp. Administration officials see that scenario as a non-starter, the official said, particularly given the fact that Dzhokhar Tsarnaev is an American citizen, naturalized last September.

AP Tamerlan Tsarnaev, left, was killed by police. Dzhokhar Tsarnaev was captured and will be interrogated by a special team of investigators.

Republican Sens. Lindsey Graham of South Carolina and John McCain of Arizona issued a statement late Friday urging that the administration hold Tsarnaev as an enemy combatant.

"It is absolutely vital the suspect be questioned for intelligence gathering purposes. We need to know about any possible future attacks which could take additional American lives," said the statement, posted on Graham's Facebook. "The least of our worries is a criminal trial which will likely be held years from now."

Mass of evidence

At the same time they are seeking to uncover the bombing suspects’ motives and determine whether they had a support network, investigators will continue to collect and analyze vast amounts of forensic evidence from crime scenes stretching across three cities.

In addition to processing evidence from the bombings, FBI technicians will analyze hundreds of hours of video camera recordings from private and public surveillance and traffic cameras as they attempt to trace the brothers’ movements – both after the attack and before it.

Investigators also will obtain and assess phone records, seeing who the brothers were in contact with in the weeks and months leading up to the attacks.

Only when they have scrutinized every bit of data, and explored every lead, will they turn over the mountain of evidence they have assembled to prosecutors. It will be up to them to decide what charges the younger Tsarnaev should face and whether to seek the federal death penalty in a state where life in prison is the maximum sentence that can be imposed.

But despite such a massive expenditure of time and technological know-how, they may never answer the most haunting question surrounding the case, as President Barack Obama noted.

“Why,” he asked during a brief statement on Dzhokhar Tsarnaev’s arrest late Friday, “did young men who grew up and studied here as part of our communities and country resort to such violence?”

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