Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, is a mild-mannered man who believes in building ties of trust with our military allies.

He’s invested many hours over the past four years in developing a relationship with Pakistan’s army chief, Gen. Ashfaq Kayani, whose help we need to end the Afghan fighting. Over and over, he and other U.S. officials urged Pakistan to cease providing havens for Afghan militants such as the Haqqani network, who kill U.S. soldiers. During the last year, when U.S. patience with Pakistan frayed, Mullen still played good cop.

Those days are over.

The chairman charged, at Senate Armed Services Committee hearings last week, that Pakistan’s ISI spy agency had helped the Haqqanis attack the U.S. Embassy in Kabul on Sept. 13. The message couldn’t have been clearer: No more Mr. Nice Guy, no more tolerating Pakistan’s double-dealing.

America is finally calling Pakistan’s bluff.

“The government of Pakistan and most especially the Pakistani army and ISI” have chosen “to use violent extremism as an instrument of policy” to extend Pakistan’s influence in Afghanistan, Mullen said. Pakistan “supported and protected” the Haqqanis, and the ISI used them as a “strategic arm,” he added. He said there was “ample evidence” the Haqqanis were also behind an attack on Kabul’s Intercontinental Hotel and a truck bomb that injured 77 U.S. soldiers near Kabul. Supporting such groups not only undermines U.S. interests but jeopardizes “Pakistan’s opportunity to be a respected and prosperous nation.”

And — in a punchline — Mullen said this behavior could warrant international sanctions. Defense Secretary Leon Panetta added that we’d “do everything we have to do to defend our forces.” He did not spell out whether that meant going after the Haqqanis with U.S. special forces and/or drones, or cutting military aid.

Given the full-court press on Pakistan last week (CIA chief David Petraeus gave the same message to ISI chief Ahmed Shuja Pasha), you might ask why U.S. officials have tolerated Pakistan’s duplicitous behavior for so long.

The answer: We’ve needed Pakistan as an ally and kept hoping fruitlessly that we could build on common interests. U.S. officials also feared that terrorists might get hold of Pakistan’s nuclear weapons, and wanted to keep close ties.

President Ronald Reagan needed Pakistan as a base from which we, and they, armed and trained Afghan mujaheddin to fight the Soviet Union. After 9/11, President George W. Bush needed Pakistan’s cooperation to hunt al-Qaida and move supplies to our troops in Afghanistan. President Obama needs Pakistan to go after al-Qaida and Taliban who use its tribal areas as sanctuaries.

Yet for years, U.S. officials have known they were being played.

Ever since 9/11, U.S. officials have urged Pakistan to shut down Taliban sanctuaries, arrest Taliban leaders, and find Osama bin Laden. Pakistani officials denied the presence of top Taliban or bin Laden, but would throw the Americans a bone by arresting an occasional al-Qaida leader.

In reality, Pakistan’s military look on militant groups as a hedge against India and as proxies who could control Afghanistan after the Americans left.

Matters came to a head in May, when a U.S. team killed bin Laden, who was hiding in the garrison town of Abbottabad. I’ve yet to meet a senior U.S. official who doesn’t believe that some ISI officials knew his location. There were no escape tunnels under his hideout, convincing U.S. officials that he expected to be tipped off by Pakistan’s military before any raid.

The attack on the U.S. Embassy was the final straw. U.S. officials are also investigating a possible ISI role in last week’s assassination of former Afghan president Burhanuddin Rabbani, who was trying to engage the Taliban in peace talks. Pakistan’s military has indicated they want a lead role in such talks, and reject independent Afghan moves.

Now that Mullen has issued the challenge, the Obama team can’t afford to let up the pressure. If U.S. officials back off now, Pakistan will continue to play the same game.

The United States must deliver this blunt message: Pakistan’s military lied to Reagan when it said it wasn’t making nukes or permitting A.Q. Khan to sell its nuclear secrets; it lied to Bush when it said bin Laden wasn’t in Pakistan. So, no one will believe it isn’t backing the Haqqanis and doesn’t know where to find their leaders — despite Kayani’s denials.

The ISI may consider the militants to be useful proxies, but they have become a Frankenstein monster that is threatening to devour the military that trained them, and is undermining Pakistani institutions. Kayani and Pasha may think they can fight some Taliban (who’ve attacked their troops) but can foster others. They are wrong; this tack poses an existential danger to their country and their nuclear weapons.

It also undercuts U.S. effort to leave behind a stable Afghanistan after 2014.

We want Pakistan as an ally, but this is intolerable behavior. If Pakistan won’t go after the militants who threaten them, us, and the Afghans, we will.