As the extraordinary manhunt for a suspected terrorist played out in Boston, officials on the scene were focused on the unfolding operation. But back in Washington some officials were already warily turning their attention to the second-guessing and finger-pointing that inevitably follows a terrorist incident.

Throughout the intelligence community, officials were scouring terrorist watch lists and monitoring intercepted conversations to learn anything they could about the origins of the attack and whether any threat remained. But one intel professional conceded that they were simultaneously looking out for any evidence that the government could have missed any advanced warnings or failed to connect the dots in the days or weeks before the Boston attacks. “At this point it’s just part of the ritual,” the source told The Daily Beast. “It goes with the territory.”

So far, nothing has emerged publicly to suggest there has been an intelligence failure of any sort. The administration—and especially the FBI—has gotten high marks for its handling of the Boston bombings. President Obama had been widely praised for his firm but restrained public response.

In the first days after a national tragedy like Boston, the country generally rallies around the flag, unites behind law enforcement, and empathizes with the victims of the violence. The media, for its part, is too preoccupied with gathering the basic facts of a fast-moving story—and placing it in some context—to raise questions about how the government might have erred.

But the Obama administration knows the honeymoon won’t last. They will have to contend with the “what did they know and when did they know it” phase of the story soon enough. And in this highly polarized climate—particularly in the emotionally charged area of terrorism—Obama officials are fatalistically preparing for an onslaught of questions and recriminations.

A case in point: senior officials at the Justice Department are even anticipating questions about whether they should have approved the use of drones to target Dzhokhar Tsarnaev, the suspected terrorist on the loose in suburban Boston. The issue caused a considerable kerfuffle last month and even led to a 13-hour filibuster by Sen. Rand Paul, who used the parliamentary maneuver to block John Brennan’s nomination to head the CIA. The Obama administration invited the questions about drones being deployed here at home by, at first, declining to rule out the possibility. To end the standoff, Attorney General Eric Holder Jr. had to write a letter to Paul assuring him that the president did not have the authority “to use a weaponized drone to kill an American not engaged in combat on American soil.” Paul ended his filibuster and declared victory.

But a case could be made that with the marathon bombings and the killing of an MIT security officer, Tsarnaev was engaged in combat on U.S. soil. The idea that the Obama administration would ever consider authorizing a drone strike in the suburbs of an American city seems absurd. But when it comes to terrorism there are few questions that would shock them—and the questions are bound to come from every direction.

“It’s a fact of life now, given the political tension over terrorism investigations that we’ve lived through over the last four years, that Justice, FBI, and White House officials—while they are laser-focused on getting this guy—are thinking about the inevitable questions Congress and the press will be asking,” says a former senior Obama Justice Department official.

“If he’s taken down, Congress and the press will ask if we could have legally used drones,” the source says. “If he’s arrested, Mirandized, and prosecuted in civilian court, they’ll ask, ‘Should he have been tried in a military commission and sent to Guantánamo?’ Suddenly all these questions will be fair game because certain critics of the administration have simply lost their bearings when it comes to the investigation and prosecution of terrorism cases.”

Of course there have also been times when the Obama national-security team has opened itself up to legitimate questions about how competently it handled a terrorist incident. Hours after the underwear bomber attempted to take down a commercial plane on Christmas Day 2009, evidence surfaced that the intelligence community failed to heed multiple warnings of the impending attack. A few days later, Obama himself chastised his national-security “principals” at a cabinet meeting. “This was a screw-up that could have been disastrous,” he told them. “We dodged a bullet, but just barely … and that is unacceptable.”

Now, as they continue to investigate the days of terror in Boston, Obama officials are bracing for a lot of questions—fair or not.