然而，九一一委员会在2003年10月18日的题为“FBI交易简报”（FBI Briefing on Trading）的备忘录中表示，当被问及媒体对硬盘恢复工作的报道时，“所有（FBI）特工都表示对所报道的硬盘恢复工作一无所知”，并进一步指出，一名纽约特工辩称：“硬盘能保存下来，里面的数据还能恢复，这没什么可能。”[25]
FBI特工兼基地组织专家约翰·P·奥尼尔（英语：John P. O'Neill）在2000年发出警告，称基地组织会对美国构成威胁。他在2001年中退休，因为FBI官员屡次阻挠他对基地组织的调查。从FBI退休后，世贸中心聘请他担任了安全主管。他于2001年8月23日开始工作；九一一救援人员在南塔废墟的楼梯间找到了他的尸体。[55]
也有指控称，劫机者的准备工作可能得到了美国情报部门的协助。据CBS新闻报道：“2000年住在圣迭戈的两名九一一劫机者，从一名据称是FBI卧底线人的男子那里租了一间房……该线人与他们一同祈祷，甚至帮助其中一人开设了银行账户。”[59]有人对快速确认劫机者身份提出了质疑，因此有人猜测FBI事先已经知道了劫机者的名字。理查德·A·克拉克（英语：Richard A. Clarke）在其《对抗所有敌人》（Against All Enemies）一书中说，9月11日上午9:59，即世贸中心2号楼倒塌的时候，也就是在美国防空司令部得知93号航班被劫持之前8分钟，FBI就已经拿到了19名劫机嫌犯的名单。一位前高级情报官员说：“不管留下了什么痕迹，都是故意留下的——以便FBI追踪。”[60]
2010年12月22日，在一次公开的法庭听证会上，一名美国联邦法官签署了一项缺席审判书，判定伊朗、塔利班和基地组织应当负责。在听证会上，原告律师提供了证据，称这些证据表明伊朗协助了劫机者。某些九一一委员会成员及证人也在听证会上作证，他们自称是伊朗叛逃者，来自伊朗情报与国家安全部及伊斯兰革命卫队。菲奥娜·哈夫利什（Fiona Havlish）的丈夫在北塔丧生，她于2001年对本·拉登等人提起诉讼。阿布加西姆·梅斯巴希（Abolghasem Mesbahi）自称是前伊朗情报部特工，负责伊朗在西欧的间谍活动。他作证说，他是专门设计对美国发动非常规战争的应急计划工作组成员，该计划的代号为“火焰撒旦”（Shaitan dar Atash），计划包括劫持客机撞击世贸中心、五角大楼和白宫；2001年夏天，他收到了三条加密消息，要求他启动该计划。他提交了一份伊朗政府的备忘录作为证据，证明伊朗宗教领袖哈梅内伊事先知道袭击事件。[64][65]裁决公布几天后，伊朗外交部发言人表示，有关伊朗“参与策划袭击以及一名基地组织成员在伊朗境内的指控毫无根据”，并表示“美国为实现其政治目的而一再重复此类指控，正将世界和平与安全置于危险之中”。[66]
这五名男子在城市搬家系统公司（Urban Moving Systems Inc）工作，该公司的老板是多米尼克·苏特（Dominik Suter）。这些人被捕后，FBI搜查了他们的办公室并询问了苏特，然而苏特在接受进一步询问之前逃往了以色列。最终，苏特的名字与九一一劫机者和其他极端分子嫌疑人一起，出现在了2002年5月的FBI嫌疑人名单上。[72]
2007年12月5日，法国当局对《世界报》记者纪尧姆·达斯奎（英语：Guillaume Dasquié）提出初步指控，指控其泄露与九一一劫机事件有关的国家机密。达斯奎曾于4月16日在《世界报》发表了题为《九一一：法国人早就知道》（September 11: the French had long known）的文章称，法国对外安全总局（DGSE）早在九一一事件发生前8个月就警告美国，基地组织可能正在策划一起恐怖阴谋，要劫持飞机并撞向大楼。该文章摘录了DGSE一份关于基地组织活动的328页机密报告，其中包括地图、分析、图表和卫星照片。[84]
常被引用的一条消息是，旧金山市长威利·刘易斯·布朗（英语：Willie Brown (politician)）在9月10日晚收到警告后，取消了9月11日的飞行计划，他说警告来自于其机场安保人员。[86]实际上，是布朗先给其在机场的安保人员打电话的，让他们检查其次日早上将要搭乘的飞机，然后他们就警告他要小心飞行。布朗说，“当我应当小心的时候，他们总是提醒我”，但他还是决定按计划飞。2006年9月，威利·布朗回应这些不断升级的阴谋论谣言，称其为“持续的神话”。
^原文：The FBI had advance indications of plans to hijack U.S. airliners and use them as weapons, but neither acted on them nor distributed the intelligence to local police agencies. From the moment of the September 11 attacks, all high-ranking federal officials insisted that the terrorists' method of operation surprised them. Many continue to stick to that story. Actually, elements of the suicide hijacking plan were known to the FBI as early as 1995 and, if coupled with current information, might have uncovered the plot.
^原文：In the two years before the September 11 attacks, the North American Aerospace Defense Command conducted exercises simulating what the White House says was unimaginable at the time: hijacked airliners used as weapons to crash into targets and cause mass casualties. One of the imagined targets was the World Trade Center. In another exercise, jets performed a mock shootdown over the Atlantic Ocean of a jet supposedly laden with chemical poisons headed toward a target in the United States. In a third scenario, the target was the Pentagon – but that drill was not run after Defense officials said it was unrealistic.
^原文：We heard of the idea of planes as weapons, but I don't recall being presented with any specific threat information about an attack of this nature, or highlighting this threat, or indicating it was more likely than any other.
^原文：Examination of the option trading leading up to September 11 reveals that there was an unusually high level of put buying. This finding is consistent with informed investors having traded options before the attacks.
^原文：Never before on the Chicago Exchange were such large amounts of United and American Airlines options traded. These investors netted a profit of at least $5 million after the September 11 attacks. Interestingly, the names of the investors remain undisclosed and the $5 million remains unclaimed in the Chicago Exchange account.
^原文：Highly publicized allegations of insider trading in advance of 9/11 generally rest on reports of unusual pre-9/11 trading activity in companies whose stock plummeted after the attacks. Some unusual trading did in fact occur, but each such trade proved to have an innocuous explanation. For example, the volume of put options — investments that pay off only when a stock drops in price — surged in the parent companies of United Airlines on September 6 and American Airlines on September 10 — highly suspicious trading on its face. Yet, further investigation has revealed that the trading had no connection with 9/11. A single U.S.-based institutional investor with no conceivable ties to al Qaeda purchased 95 percent of the UAL puts on September 6 as part of a trading strategy that also included buying 115,000 shares of American on September 10. Similarly, much of the seemingly suspicious trading in American on September 10 was traced to a specific U.S.-based options trading newsletter, faxed to its subscribers on Sunday, September 9, which recommended these trades. These examples typify the evidence examined by the investigation. The SEC and the FBI, aided by other agencies and the securities industry, devoted enormous resources to investigating this issue, including securing the cooperation of many foreign governments. These investigators have found that the apparently suspicious consistently proved innocuous.
^原文：During the spring and summer of 2001, U.S. intelligence agencies received a stream of warnings about an attack al-Qaeda planned, as one report puts it "something very, very, very big." Director of Central Intelligence George Tenet told us "the system was blinking red."
^原文：Mr. Speaker, I rise because information has come to my attention over the past several months that is very disturbing. I have learned that, in fact, one of our Federal agencies had, in fact, identified the major New York cell of Mohamed Atta prior to 9/11; and I have learned, Mr. Speaker, that in September 2000, that Federal agency actually was prepared to bring the FBI in and prepared to work with the FBI to take down the cell that Mohamed Atta was involved in in New York City, along with two of the other terrorists. I have also learned, Mr. Speaker, that when that recommendation was discussed within that Federal agency, the lawyers in the administration at that time said, you cannot pursue contact with the FBI against that cell. Mohamed Atta is in the U.S. on a green card, and we are fearful of the fallout from the Waco incident. So we did not allow that Federal agency to proceed.
^该谣言来自《耶路撒冷邮报》9月12日的网络版上，文中称：“The Foreign Ministry in Jerusalem has so far received the names of 4,000 Israelis believed to have been in the areas of the World Trade Center and the Pentagon at the time of the attacks.[耶路撒冷外交部迄今已收到了一份4000名以色列人的名单，据信他们在袭击发生时正身处世贸中心和五角大楼附近。]”
^Geheimsache World Trade Center [世界贸易中心的秘密]. 德国电视二台新闻. 2002-03-11 （德语）.
^九一一委员会. FBI Bfiefing on Trading [FBI交易简报](PDF). 2003-10-18 [2011-05-03]. （原始内容(PDF)存档于2011-05-31） （英语）. The assembled agents expressed no knowledge of the reported hard-drive recovery effort or the alleged scheme. Moreover, one of the New York agents pointed out, from personal experience, that everything at the WTC was pulverized to near power, making it extremely unlikely that any hard-drives survived to the extent they data be recovered.[在场的特工表示，对所报道的硬盘恢复工作或所谓的阴谋一无所知。此外，一位纽约特工根据个人经验指出，世贸中心的所有东西都被粉碎得几乎无法恢复。因此，硬盘能保存下来，里面的数据还能恢复，这没什么可能。]
^Allen M. Poteshman. Unusual Option Market Activity and the Terrorist Attacks of September 11, 2001 [期权市场的异常活动与九一一恐怖袭击]. 商业杂志: 670—675. JSTOR 10（英语）.
^Marc Chesney; et al. Detecting Informed Trading Activities in the Options Markets [对期权市场中知情交易活动的检测]. 社会科学研究网. 2010年1月. SSRN 1522157（英语）.
^Wing-Keung Wong; et al. Was there Abnormal Trading in the S&P 500 Index Options Prior to the September 11 Attacks? [九一一袭击事件前标普500指数期权是否存在异常交易？]. 社会科学研究网. 2010年4月. SSRN 1588523（英语）.
^Neil A. Lewis. F.B.I. Chief Admits 9/11 Might Have Been Detectable [FBI局长承认九一一可能已被探测到]. 纽约时报. 2002-05-30 [2024-06-19]. （原始内容存档于2016-05-12） （英语）. ...reassigning 400 of the bureau's 11,500 field agents from narcotics investigations to counterterrorism. Another 59 agents would be reassigned to counterterrorism from white-collar crime investigations and an additional 59 from the violent crimes unit.[……将局内11,500名外勤特工中的400名从毒品调查部门调往反恐部门。还有白领犯罪调查部门的59名特工，以及暴力犯罪部门的59名特工都被调往反恐部门。]
^凯特·克拉克（英语：Kate Clark (journalist)）. Taleban 'warned US of huge attack' [塔利班“向美国发出了大规模袭击警告”]. BBC新闻. 2002-09-07 [2007-01-16]. （原始内容存档于2007-08-25） （英语）. An aide to the former Taleban foreign minister, Wakil Ahmad Muttawakil, has revealed that he was sent to warn American diplomats and the United Nations that Osama bin Laden was due to launch a huge attack on American soil.[塔利班前外交部长瓦基勒·艾哈迈德·穆塔瓦基勒的助手透露，他奉命向美国外交官和联合国发出了警告，称奥萨马·本·拉登将对美国本土发动大规模袭击。]
^Susan Lindauer Speaks in Seattle [苏珊·林道尔在西雅图发声]. YouTube. [2011-09-17]. （原始内容存档于2023-11-21） （英语）. And I said, "you think it's that soon?" And he said, "oh, it's just in a couple weeks." And I said, "oh, well, I'll go back to New York and I'll talk to the Iraqi diplomats immediately and see if they've got any word from Baghdad. I'll try one more time." And he said, "Susan, don't go back to New York. Do not go back to New York!" And I said "Richard, you think it's going to be that soon?" and he said "yeah, I don't want you going back to New York at all, until this is over." And I said, "well, I'll go up the day after tomorrow," which was August 4th. And he said "after that, never again until it's done."[我说：“你觉得会这么快吗？”他说：“哦，只要再过几周。”我说：“哦，好吧，我要回纽约，马上跟伊拉克外交官谈谈，看看他们有没有收到巴格达的任何消息。我会再试一次。”他说：“苏珊，别回纽约。别回纽约！”我说：“理查德，你觉得会这么快吗？”他说：“是的，在这事结束之前，我根本不想让你回纽约。”我说：“好吧，我后天去，”也就是 8 月 4 日。他说：“之后再也别去了，直到这事结束。”]
