U.S. justifications for Iran war not discussed: Ongoing Iranian protection of al-Qaeda leaders

The Trump Administration has listed dozens of examples of Iranian terrorism aimed at American citizens and soldiers over the past nearly five decades, but a significant omission was the Iranian regime’s decades-long (and likely ongoing) protection of key al-Qaeda leaders following the terrorist attacks of 9/11.The White House in early March released a lengthy fact sheet titled “The Iranian Regime’s Decades of Terrorism Against American Citizens.” The Trump administration document laid out Iran’s lengthy history of targeting and attacking U.S. troops, diplomats, and citizens. The White House’s Rapid Response X account also put out a lengthy tweet thread on the topic. While extensive in its listing of Iran’s history of supporting terrorism since 1979, it did not mention the regime’s close current relationship with al-Qaeda.
Under Iran’s protection
Just the News reported in late February — just days before Trump announced U.S. strikes against the Iranian regime and its military — that the U.S. and a specialized United Nations team previously assessed that the FBI’s “Most Wanted” Saif al-Adel has been running the global terror network under Tehran’s protection.
Iran’s assistance even before 9/11 to al-Qaeda has been highlighted by Trump and by his White House. The White House fact sheet from early March lists one such deadly attack in particular: “August 1998: Al-Qaeda suicide bombers, facilitated by Iran-backed Hezbollah, simultaneously bombed U.S. embassies in Kenya and Tanzania, killing 224 people — including a dozen American citizens.”
Just the News reported this week that Trump himself has also repeatedly argued in recent days that the Iranian regime bears some responsibility for the terrorist suicide bombing of the USS Cole in 2000, during which al-Qaeda terrorists used an explosive-laden boat to conduct a suicide attack which killed 17 U.S. sailors. The president has gotten pushback from some in the press about making this linkage, but a federal judge has repeatedly agreed with him that Iran was “complicit” in the attack.
Yet neither the White House nor any key Trump administration officials seem to have raised Iran’s close and ongoing post-9/11 relationship with al-Qaeda, including the regime’s shielding of multiple top al-Qaeda leaders for more than two decades.
The White House did not immediately respond to a request for comment.
“The Iranian regime’s blood-soaked war on Americans”
“For nearly half a century, the Islamic Republic of Iran — the world’s leading state sponsor of terrorism — has killed and maimed American citizens and service members through its own forces and proxy militias. More Americans have been killed by Iran than any other terrorist regime on Earth,” the White House fact sheet said.
The White House document published early this month said that what it was releasing was “only a partial record of the Iranian regime’s blood-soaked war on Americans” but it was notable that the Shiite Iranian regime’s protection of the Sunni jihadist terrorist group’s leaders after 9/11 was not mentioned.
Examples included from the White House include Iran taking U.S. diplomats hostage for 444 days starting in 1979, its involvement in the suicide truck bombing of the U.S. Embassy in Beirut in April 1983, the deadly bombing of the U.S. Marine barracks in Beirut in October 1983, the bombing of the U.S. Embassy annex in Beirut in September 1984, the hijacking of TWA 847 in 1985, the Khobar Towers attack in Saudi Arabia in 1996, and much more.
Just the News also previously reported that the White House fact sheet detailed Iran’s role in the deaths of more than 600 U.S. service members during the war in Iraq, but that it made no mention of the Iranian regime’s similar documented history of helping the Taliban kill U.S. and NATO forces in Afghanistan for nearly two decades.
Nukes, missiles, and proxies scrutinized — but sheltering al-Qaeda not mentioned
Much of the discussion around the current war with Iran has focused on the Iranian regime’s nuclear program, its ballistic missiles, and its support for terrorist proxies like Hamas, Hezbollah, and the Houthis — but little attention has been paid to Iran hosting al-Qaeda operatives, including its newest chief, inside the country for many years.
“Iran is clearly sheltering Iran’s top leadership. Iran views al-Qaeda as an important tool in its efforts to undermine the U.S. and the West in the Middle East,” Bill Roggio, a senior fellow at the Foundation for Defense of Democracies (FDD), told Just the News last month. “By sheltering Saif Al-Adel, Iran ensures continuity for al-Qaeda’s leadership, and he essentially is untouchable unless the U.S. actually decides to go after him in Iran.”
Roggio, who is also the editor of FDD’s Long War Journal, added that “Saif Al-Adel has been reported to travel between Iran and Afghanistan, but I assess that he is primarily based in Iran” and that “Iran provides Al-Qaeda with a base of operations for its global leadership.”
Despite theological differences, the Iranian regime has a long history — both before and after 9/11 — of collaborating with al-Qaeda, with the two displaying some ideological flexibility in working together against the West. The DOJ and U.S. investigators have pointed to links between al-Qaeda, Hezbollah, and the Iranian regime during the pre-9/11 era. The State Department and other agencies have repeatedly lamented over many years that Iran has continued to shield al-Qaeda operatives inside their country after 9/11.
Federal courts in the U.S. have also concluded that Iran used al-Qaeda as a tool against the U.S. before 9/11 and assisted the terrorist group and the Taliban in their successful efforts to evict the U.S. from Afghanistan.
Edmund Fitton-Brown, also a senior fellow at FDD and the former British ambassador to Yemen, told Just the News last month that “Saif is believed still to be in Iran” and that “he has encouraged fighter migration to Afghanistan, but that doesn’t mean he himself is there.”
Rep. Blake Moore, R-Utah, was one of the few government officials in pointing to Iran’s connections to the jihadist group in recent days, stating in early March that “Iran provided a safe harbor to al-Qaeda militants immediately after the 9/11 attacks and allowed its senior leaders to base their operations there.”
Al-Qaeda leader has been hiding out in Iran for more than two decades
The FBI’s “Most Wanted” notice about Saif says that he is “an Iran-based al-Qaeda senior leader and a leader of the Hittin Committee, which governs and coordinates the group’s transnational activities.” The UN has said that as early as 2015 operational and financial connections with al-Qaeda regional affiliates were facilitated.
The State Department’s “Rewards for Justice” page says that Saif “moved to southeastern Iran and lived under the protection of Iran’s Islamic Revolutionary Guard Corps” after the 1998 bombings of the U.S. embassies. The reward page says that “Iranian authorities placed him and other AQ leaders under house arrest” in 2003, and that Saif “and four other senior AQ leaders were released from Iranian custody” in 2015 “in exchange for an Iranian diplomat kidnapped by AQ in Yemen.”
The Long War Journal reported in 2011 that Saif “has a decades-long relationship with Iran” and that, after 9/11, the terrorist “fled to Iran along with other al Qaeda operatives. He was eventually placed in a loose form of house arrest after American and Saudi intelligence officials complained about his links to international attacks, including the May 2003 Riyadh bombings.” The outlet said that Saif “was freed by Iran in 2010” but remained there under the regime’s protection.
“Ayman al-Zawahiri, partly through the agency of senior al-Qaeda leadership figures based in the Islamic Republic of Iran, Abu Muhammad Al-Masri and Saif Al-Adel, has been able to exert influence on the situation in north-western Syrian Arab Republic,” a UN report said in 2018.
Masri had been al-Qaeda’s number two under Zawahiri but was shot to death in Tehran in 2020.
Pompeo: “Al-Qaeda has a new home base”
Then-Secretary of State Mike Pompeo announced in January 2021 — in the final days of Trump’s first term — that “al-Qaeda has a new home base: it is the Islamic Republic of Iran. As a result, bin Laden’s wicked creation is poised to gain strength and capabilities. We ignore this Iran and al-Qaeda nexus at our own peril.”
Pompeo said then that al-Qaeda “has centralized its leadership inside of Tehran” and so “al-Qaeda terrorists like Saif al-Adel and the now-dead Abu Mohammed al-Masri have been able to place a new emphasis on global operations and plotting attacks all across the world.”
Photographic evidence of Saif and two other al-Qaeda leaders living in Tehran emerged in 2022, with the picture allegedly dating back to 2015 or earlier. The Long War Journal said that two U.S. intelligence officials independently confirmed the authenticity of the picture. The Long War Journal has also noted that “members of Osama’s family, including his son Hamza, fled to Iran after 9/11 as well.”
Christine Abizaid, then the director of the National Counterterrorism Center, said in 2022 that “in addition to al-Qaeda affiliate leaders, we are particularly focused on the role that Iran-based legacy leaders, such as Saif al-Adel, may play in the future of the organization.”
Iran has denied the presence of al-Qaeda leaders within the country
“The Islamic Republic of Iran categorically rejects the claim that members of al-Qaeda, including its so-called leader, Saif al-Adel, are present in Iranian territory,” Iran said in a letter to the UN in March 2025. “The report’s cynical attempt to link the Islamic Republic of Iran with al-Qaeda is entirely unprofessional, unsubstantiated, and detached from reality.”
The UN specialized monitoring team said in 2023 that the “predominant view” of UN member countries was that Iran-based Saif was “now the de facto leader” of al-Qaeda and that his leadership was “uncontested.”
The UN team repeated in 2023 that “some Member States assessed that Saif al-Adel is most likely to succeed Ayman al-Zawahiri and reportedly still in the Islamic Republic of Iran.” The Treasury Department’s National Terrorist Financing Risk Assessment said in 2024 that “U.S. and UN officials have confirmed that AQ’s new leader, Saif al Adel, is currently residing in Iran.”
The Soufan Center assessed last year that “while al-Qaeda core remains hobbled by the attrition of its senior leadership, some of which is still believed to be based in Iran, including its de facto head Saif al-Adel, taking this organization or any of its regional branches for granted is a recipe for disaster.”
The Defense Intelligence Agency stated in its 2025 Worldwide Threat Assessment that al-Qaeda “never officially named a successor” to Zawahiri after his death in 2022, assessing that the terrorist group’s “probable acting emir” was the “Iran-based Saif al-Adl.”
Fitton-Brown said “The reason that this is so critically important is that al-Qaeda is increasingly becoming at least a partial member of the Iranian axis of resistance, and if we’re about to have another conflict with Iran, which we might be, and even if we don’t — because the other possibility is that the U.S. kind of walks away from the current standoff and the Iranians start rebuilding and figuring out what they can do to continue to attack their enemies — well, they are going to rely more and more on proxies,” Fitton-Brown said.
Al-Qaeda uses conflict with Iran to urge jihad against the U.S.
The Middle East Media Research Institute (MEMRI) reported in early February that al-Qaeda had released a statement condemning America’s potential war with Iran. “Al-Sahab, the official media arm of al-Qaeda’s central command, released a statement titled ‘Learn From This, You Who Can See.’ The statement argues that a ‘Zionist-Crusader’ coalition against Islam is once again mobilizing and urges Muslims to rise against American forces in the Middle East and against Israel,” MEMRI said.
Al-Qaeda condemned “Crusader America” and its “Crusader Project” as it called for the mobilization of a jihad against the “Crusader hordes.” MEMRI added that the al-Qaeda messaging urged jihadists to target U.S. aircraft carriers that “the people of jihad can sink, as did the knights of Islam in Yemen” when al-Qaeda bombed the USS Cole in 2000.
Reichman University’s International Institute for Counter-Terrorism said in early February that “al-Qaeda is calling for a jihadist war against the American presence in the region and for halting what it describes as a U.S.-led Jewish crusade against Muslim lands and the religion of Islam.”
“Al-Qaeda’s call for jihad against the United States is an opportunistic attempt to exploit tensions between Washington and Tehran in order to restore its relevance in the cognitive and ideological sphere,” the university’s institute said. “The organization frames the regional escalation as proof of its long-standing narrative of a ‘Western war against Islam,’ aiming to legitimize violence and mobilize supporters, even though its actual ability to influence the strategic balance remains limited.”
Cambridge University’s Elisabeth Kendall in early February said that “the General Leadership of al-Qaeda has released a new statement condemning the amassing of US forces in the Gulf.”
“It tries to frame this as part of a broader and ongoing Zionist-Crusader project to occupy Muslim lands (rather than a threat specifically directed at Iran),” Kendall tweeted. “In this way, it can justify a call to arms in defense of Islam (not Iran).”
The Small Wars Journal last week said that “Al-Qaeda’s latest statement suggests another possibility: that the time has come for Iran to cash in on its long-term investment in al-Qaeda, bringing the group into the broader regional conflict.”
The outlet also posited that “Al-Qaeda’s declaration of jihad against U.S. military may be an attempt to prove its loyalty to Tehran — a signal that, despite sectarian differences, they stand united against a common foe.”
It was reported by the Sunday Times on Monday that “social media channels affiliated with al-Qaeda have put out messages supporting Iran in the war and any cells or followers they have left might be tempted to push forward plans to attack western targets.”
Worries about Iran potentially using Al-Qaeda as a proxy
West Point’s Combating Terrorism Center warned in September that “there is also a possibility that Iran looks to help al-Qaeda reassert its relevance by providing the group with intelligence, weapons, and training.”
“After all, Tehran has provided a safe haven to Saif al-Adel and other senior members of the group for the last two decades,” the center said. “At some point, Iran will want to benefit from the relationship. Following the recent joint U.S.-Israeli assault on Tehran’s nuclear infrastructure, which came five years after the targeted assassination of Islamic Revolutionary Guard Corps Quds Force commander Qassem Soleimani, this could be a logical time for Iran to activate or enable al-Qaeda, as there are already growing connections between members of Iran’s ‘Axis of Resistance’ and al-Qaeda affiliates al-Shabaab and AQAP.”
The West Point center assessed that “this, in turn, could create a contagion effect that facilitates terrorism, or terror actors, in other neighboring regions to become more active.” The New York Times reported late last month that “there is also concern in Europe that Hezbollah sleeper cells or even al-Qaeda or its affiliates could be ordered to attack American bases or embassies.”
“In a war between Iran and the United States, some analysts believe Qaeda operatives could be directed to carry out terrorist attacks in Europe or the Middle East,” the outlet said. “Last year there were heightened concerns that the group was planning an attack, a federal law enforcement official said.”
Al-Qaeda’s current ties to Iran may be behind group’s growing ties to the Houthis
Fitton-Brown, also the former coordinator for the United Nations team responsible for sanctions and threat assessment on the Taliban and terrorist groups like ISIS and al-Qaeda, told Just the News last month that Saif’s presence in Iran “is one reason for the continuing deconfliction” between al-Qaeda in the Arabian Peninsula and the Houthis as well as “the emerging AQAP-brokered relationship” between the Houthis and al-Qaeda-linked Al-Shabaab in Somalia.
West Point’s Combating Terrorism Center said in September that al-Qaeda “has successfully built a global network that spans decades and dozens of countries, demonstrating a superior aptitude for alliance building” and that “now, its affiliates are doing the same. Increasing cooperation between Somalia-based al-Shabaab and Iran-backed Yemen-based Ansar Allah (the Houthis) is a case in point.”
“Since 2024, evidence has emerged that al-Shabaab receives arms and training in exchange for Houthi piracy operations off the coastline of Somalia it controls,” the center assessed. “Meanwhile, in Yemen, AQAP has not only ceased hostilities with Ansar Allah but has also begun cooperating with the group in launching joint attacks against government forces. This apparent de-prioritization of ideology, often due to strategic necessity, has been observed across theaters.”
The UN Panel of Experts on Yemen similarly found in 2024 that “the increasing collaboration between the Houthis and terrorist groups like Al-Qaeda in the Arab Peninsula is concerning.”
“Both have agreed to cease internal conflict, transfer weapons and coordinate on attacks against the forces of the Government of Yemen,” the panel concluded. “In addition, increased smuggling activities involving small arms and light weapons are observed between the Houthis and Al-Shabaab, with indications of shared military supplies or a common supplier.”
Calls for the U.S. to confront Iran for shielding al-Qaeda
Joe Zacks, the retired deputy assistant director for counterterrorism at the CIA, wrote a piece for the National Interest in late February where he insisted that “Iran’s nuclear program is at the heart of its ongoing standoff with the United States, but Washington also needs to confront Iran on another key issue: its persistent support for al-Qaeda and its ongoing relationship with the Taliban.”
“The U.S. is currently examining all options, from negotiations to kinetic action, to force Iran to curb its menacing actions in the region or face the hastening of regime change. One urgent U.S. request should be the extradition of Saif al-Adel to his home country of Egypt and the removal of other al-Qaeda members known to the US intelligence community from Iran.”
Elliot Nazar, a fellow at the Middle East Forum, wrote on Tuesday that “amidst the United States and Israel’s military campaign against the Islamic Republic of Iran and its terrorist proxy network, Washington has a rare opportunity to confront al-Qaeda’s presence in Tehran.”
“The Trump administration should deploy Special Operations Forces to locate Adel and other remaining al-Qaeda leaders inside Iran and bring them to justice,” Nazar argued. 
“The Trump administration also should not hesitate to target Iranian regime officials who knowingly sheltered al-Qaeda leaders and were aware of their activities inside the country. Should the administration decide to return to negotiations with Tehran, they must demand that Iran hand over the group’s remaining leaders,” he added.

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