The Bush administration waged what it called a Global War on Terrorism. Yet against Iran, the world’s leading sponsor of terrorism, no serious actions were ever taken. President Obama is waging what he calls a “war against al-Qaeda and its affiliates.” Yet he and his advisers are reluctant to articulate what has become indisputable: Iran and al-Qaeda are affiliated.

Senior Obama officials have come closer to calling a spade a spade: Last week, Director of National Intelligence James Clapper described the relationship between Iran and al-Qaeda as a “longstanding . . . marriage.” But you had to listen carefully to hear him say that.

“Iran has harbored al-Qaeda leaders, facilitators,” Clapper told a hearing of the Senate Armed Services Committee. They have been “under house-arrest conditions. [Iran’s rulers] have had this sort of standoff arrangement with al-Qaeda, allowing [al-Qaeda] to exist [inside Iran], but not to foment any operations directly from Iran, because they’re very sensitive about, ‘Hey, we might come after them there as well.’ . . . So there has been this longstanding, as I say, kind of, shotgun marriage, or marriage of convenience. I think, probably, the Iranians may think that they might use, perhaps, al- Qaeda in the future as a surrogate or proxy.”

Not quite a model of analytic clarity but, as I said, at least it approaches reality (and do note the cryptic warning about Iran deploying al-Qaeda terrorists down the road — more about that in a moment). Also last week: The U.S. Treasury Department designated the Iranian Ministry of Intelligence and Security (MOIS) — which it described as “Iran’s primary intelligence organization” — as a sponsor of terrorism. And among the terrorist groups Treasury said MOIS supports: al-Qaeda. The forms this support has taken: facilitating the movement of al-Qaeda operatives in Iran; providing al-Qaeda members “with documents, identification cards, and passports”; and providing both “money and weapons” to al-Qaeda terrorists in Iraq.

Michael Ledeen and Thomas Joscelyn, my colleagues at the Foundation for Defense of Democracies, have for years been connecting the dots between Iran and al-Qaeda. Former CIA director James Woolsey, now FDD’s chairman, also has long argued that Islamist terrorists, despite their theological and ideological differences, can and do engage in “joint ventures” to accomplish common goals.

Joscelyn has extensively researched this relationship. Back in 2007, he wrote: “No fallacy today is more misguided or more dangerous than the widespread belief that Iran, the world’s premier state sponsor of terrorism, and al-Qaeda are not allies in the terrorists’ war against the West. A corollary myth holds that Hezbollah — Iran’s terrorist proxy and the ‘A-team’ of international terrorist organizations — has also not allied itself with al-Qaeda.”

The terrorist attack that killed 19 Americans at Khobar Towers in 1996 was most likely an Iranian–al-Qaeda joint venture. But the Clinton administration chose to shut down FBI investigators in the belief — misguided but widespread at the time — that more moderate Iranians were coming to power in Tehran and that publicly revealing the Iranian role would impede diplomatic efforts.

Iran also has been implicated in al-Qaeda’s 1998 bombing of America’s embassies in Nairobi and Dar es Salaam. When federal prosecutors indicted al-Qaeda members that same year, they specifically noted that al-Qaeda had forged alliances with “representatives of the government of Iran, and its associated terrorist group Hezbollah, for the purpose of working together against their perceived common enemies in the West, particularly the United States.” And in November of last year, a Washington, D.C., court found that Iran had provided training for the al-Qaeda terrorists at Hezbollah camps in southern Lebanon. The court stated unequivocally that the “government of the Islamic Republic of Iran . . . has a long history of providing material aid and support to terrorist organizations including al Qaeda.”

What about the attacks on New York and Washington three years later? The 9/11 commissioners said they “found no evidence that Iran or Hezbollah was aware of the planning for what later became the 9/11 attack.” However, intelligence obtained by 9/11-commission staffers just before the release of their report — too late for serious examination — showed what Joscelyn called “suspicious flights taken by the muscle hijackers. Some of the flights were routed through Lebanon, where Hezbollah is based and controls the airport. Interestingly, most of the muscle hijackers also transited through Iran en route to the United States.” The commissioners wrote: “We believe this topic requires further investigation by the U.S. government.” Such investigations have not been conducted — or, if they were, their conclusions have never been made public.

In the years since 2001, Iran has continued to cooperate with al- Qaeda. In January 2009, Treasury designated four senior al-Qaeda members who had received Iran’s assistance. Among them: Saad bin Laden, one of Osama’s sons. Joscelyn records that the young bin Laden “received safe haven inside Iran after 9/11 and was placed under a loose form of ‘house arrest’ in 2003 after he was implicated in al-Qaeda attacks in Saudi Arabia and elsewhere. Saad and the other designated al-Qaeda operatives were responsible for moving al Qaeda families, including some of Osama bin Laden’s and Ayman al Zawahiri’s closest relatives, to Iran after the 9/11 attacks. Saad subsequently left Iran for northern Pakistan, where he was reportedly killed in a U.S. drone strike.”

Last July, as Joscelyn also reported, “Treasury designated six al Qaeda operatives who use a network headquartered in Iran to move cash and terrorists. Iran, Treasury noted at the time, is ‘a critical transit point for funding to support al Qaeda’s activities in Afghanistan and Pakistan.’” And in September 2011, the State Department designated a Hamas operative, Muhammad Hisham Muhammad Isma’il Abu Ghazala, linking him to both Iran and al-Qaeda.

In recent days, Britain’s Sky News has been reporting that its “intelligence sources” have strong evidence that “Iran has been supplying al-Qaeda with training in the use of advanced explosives.” Sky News claims it has seen a “secret intelligence memo” describing “intensive co-operation over recent months between Iran and al Qaeda — with a view to conducting a joint attack against Western targets overseas.” Sky News adds: “We do know that an operation is under way. We assess that the most likely target is to be European.”

In light of all this, why has there been so little public discussion of the Iranian-al-Qaeda relationship? Two reasons suggest themselves: (1) Scholars, journalists, and intelligence analysts who denied this association in the past are reluctant to admit they were wrong. (2) Knowledge conveys responsibility: If Iran is — and long has been — married to al-Qaeda, and if Iran is now just a few spins of a centrifuge away from acquiring nuclear weapons, it follows that strong measures must be taken against this growing threat.

That’s a message many Americans do not want to hear. It’s certainly a message many American leaders do not want to tell them.