Is the war on terror over?

“The war on terror is over.” That’s what a senior State Department official told the National Journal in light of the Arab spring uprisings and the killing of Usama Bin Laden.

The article’s ink was barely dry when a White House spokesman corrected the record. The State Department official had misspoken: President Obama’s “war on Al Qaeda” was being fought furiously, and would continue.

In fact, Obama rejected George W. Bush’s war on all of the violent Islamists and terrorists who might threaten America– his “Global War on Terror” – back in 2009. Instead, he had embraced a more intensely focused “war on Al Qaeda, its affiliates, and adherents.”

That this more concentrated war continues was crystal clear during a trial last week in Brooklyn featuring Najibullah Zazi, the home-grown mastermind of the 2009 Al-Qaeda plot to bomb New York’s subways. The suicide strike might have been the deadliest attack on American soil since 9/11 had the FBI and NYPD not thwarted it, police say. While Zazi and a fellow home-grown militant from Queens pleaded guilty to terror charges and testified for the government, a third alleged conspirator, Adis Medunjanin, denied guilt.

The testimony against him was an unsettling reminder that the war on terror, or Al Qaeda, or whatever else the administration calls it remains decidedly unfinished business.

That, too, was the message from John Brennan, President Obama’s senior counter-terrorism adviser, who visited New York City as the trial was getting underway.

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Brennan warned in a speech to the NYPD that Al Qaeda and other violent jihadis still threatened America. If America wanted to avoid “another devastating attack,” it could not afford to drop its guard, he said. While hundreds of key Al Qaeda operatives had been killed and its abilities severely degraded, Al Qaeda still had “several hundred” members in Pakistan and another “hundred” or so in Afghanistan. Washington remained alarmed not only about Al Qaeda “core” but also about its metastasized affiliates and adherents – first among them, Al Qaeda in the Arabian Peninsula or AQAP.

AQAP, Al Qaeda’s “most active operational franchise,” now had over a thousand members in Yemen, he said. Al Qaeda branches and affiliates and like-minded militants might also develop international agendas and capabilities. Noting the formal merger between the Somali militant group al Shabaab and Al Qaeda only two months ago, he said that Al Shabaab was now committed to Al Qaeda’s campaign of international terrorism. Another Al-Qaeda affiliate in North Africa was now operating in Algeria, Libya, Tunisia, Niger, Burkina Faso, Mauritania, and Mali.

There was no shortage of counter-terrorism frustrations, he added -- the millions of dollars that European states have paid to ransom nationals held hostage; concern that terrorists might acquire Libyan weapons from unsecured stockpiles: stopping terrorists from gravitating towards lawless areas in Egypt’s Sinai near Israel; the possibility that Al Qaeda might fill a political vacuum in Syria.

Preventing Al Qaeda from capitalizing on the chaos of the Arab Spring would require “one, two, three years” of intense focus, Brennan warned.

At home, he worried about the proliferation of homegrown militant loners, inherently more difficult to detect and stop than radical groups. The growing sophistication of AQ bombs, the result of a generation of militants schooled in Iraq and Afghanistan, could also threaten Americans in the coming decade.

In a press conference after his speech, Brennan praised the NYPD’s counter-terrorism work, asserting that New York’s finest had struck an “appropriate” balance between protecting the city and its citizens’ civil liberties.

The apparent endorsement meant much to the NYPD. The cops have been under fire from the AP, civil libertarians, and assorted Muslim activists over their aggressive Muslim surveillance program which has helped foil 14 plots against the city since Sept. 11. Critics say the department’s efforts to understand the communities in which terrorists are likely to recruit or hide constitute racial profiling and violate civil liberties guarantees. The police insist that the program is legal and essential. Brennan’s speech and subsequent remarks were widely seen as an endorsement of the NYPD’s actions.

But Brennan had barely finished speaking when White House officials once again clarified his remarks by asserting that Brennan wasn’t defending the NYPD’s controversial Muslim surveillance program at all.  “John never approved of described press accounts of alleged NYPD surveillance,” a senior official said. Rather, Brennan was noting that “everyone in the counterterrorism and law enforcement community must make sure we are doing things consistent with the law.”

I was standing next to Brennan when he was asked for his view of the NYPD’s surveillance effort. Saying that he had known and worked with Police Commissioner Ray Kelly for years, Brennan said he did not think that Kelly would violate the law. “I have full confidence that the NYPD is doing things within the law, and has been responsible for keeping this city safe for the past decade,” he said. The Muslim community was “part of the solution to the terrorist threat,” he said, and needed to be “part of that effort.”

On Sunday, the White House further clarified its earlier clarification. Brennan was indeed a “very strong supporter of the tremendous work done by NYPD on a daily basis keeping New York City safe,” National Security Council spokesman Tommy Vietor wrote. But because the Justice Department has been “reviewing requests” that the NYPD surveillance program be investigated, Brennan “did not” and would not comment, “much less pass judgment, on any of those allegations or the Justice Department’s pending review.”

This is silly. For the administration’s unwillingness to openly back the NYPD – or permit Brennan to do so – is not only at odds with Obama’s own actions, it undercuts his impressive anti-terrorism accomplishments as “warrior in chief,” as Peter Bergen, the author of a new book, “Manhunt: The Ten-Year Search for Bin Laden — From 9/11 to Abbottabad,” calls him.

Obama’s counter-terrorism achievements cannot be denied. Thanks to his gutsy call, Usama bin Laden is dead. Ditto Anwar al-Awlaki, the de facto chief of AQAP.

Al Qaeda's “core” has been decimated due to increased American drone strikes in Yemen, Pakistan and Afghanistan.

Guantanamo is still open, despite his vow on his first day in office to close it.

Obama now asserts the right not only to target American citizens for assassination without judicial review if intelligence suggests they are involved in plotting terror, but to hold some terror suspects in jail indefinitely without trial.

This year, he revised guidelines to permit law enforcement to store records on people not suspected of terror from five months to 5 years.

I don’t recall hearing demands for judicial review of such actions, however troubling to civil libertarians (including me) some of them, especially those affecting American citizens, may be.

In fact, despite his campaign pledges, Obama’s counter-terrorism policy bears a striking resemblance to President Bush’s, minus the waterboarding. That, I suspect, is precisely what troubles Obama’s liberal base and some of the officials around him.

The administration seems to want to have things both ways – to bask in the glow of its counter-terrorism achievements, while downplaying the rhetoric, mind-set, and actions that a war on terror involves.

On one hand, his spokesmen try to placate his left-wing base – by initially calling the war on Al Qaeda “overseas contingency operations,” (pathetic bureaucratic blather), by rejecting talk of a broader “war” on terror while waging one, and by trying to distance Obama from the NYPD’s aggressive, successful tactics by calling for a judicial review of the cops’ surveillance program.

On the other hand, they tout Obama’s counter-terrorism victories in ads and interviews to combat assertions from the right that Obama is weak.

Such mixed signals, however, have often angered both left and right. And Mr. Obama has been able to sustain this cognitive dissonance only because his liberal base has resisted calling him on the contradictions between his pledges and his policies.

But in an election year, voters are demanding that Obama clarify where he stands on such issues as the balance between freedom and national security.

On Monday in a speech in Washington, Brennan outlined in detail the legal, strategic and ethical rationale for using drones to target and kill suspected terrorists – foreign and American –abroad, despite the fact that innocent civilians would continue to die.

It was an impressive, and to my mind, persuasive argument. -- Voters should demand more such genuine clarifications from the president and his team.

Better late than never.

Judith Miller is a Manhattan Institute Scholar and Fox News contributor. She is a writer and award-winning journalist.