At some point after the White House is ordered to evacuate and while Air Force One is preparing to take off in Florida, counterterrorism “tsar” Richard Clarke activates the Continuity of Government (COG) plan. The coordinator for Continuity of Government has joined Clarke in the White House Situation Room. Clarke asks, “How do I activate COG?” Recalling this conversation, he will later comment, “In the exercises we had done, the person playing the president had always given that order.” But the coordinator replies, “You tell me to do it.” Soon after, Clarke instructs him, “Go.” [Clarke, 2004, pp. 8]
First Time COG Plan Activated – The Continuity of Government plan, which dates back to the Reagan administration, had originally prepared to set up a new leadership for the US in the event of a nuclear war. This is apparently the first time it has ever been put into effect. Clarke will recall, “Every federal agency was ordered… to activate an alternative command post, an alternative headquarters outside of Washington, DC, and to staff it as soon as possible.” Cabinet officers are dispatched around the country, and people in Congress are taken to alternative locations.
Clarke Regularly Particiated in COG Exercises – Since the 1980s, Clarke has in fact been a regular participant in secret COG exercises that rehearsed this plan (see (1984-2004)). [Washington Post, 4/7/2004; ABC News, 4/25/2004] Vice President Dick Cheney and Secretary of Defense Donald Rumsfeld also participated (see 1981-1992). [Atlantic Monthly, 3/2004] Kenneth Duberstein, formerly President Reagan’s White House chief of staff, who took part in the exercises as well, will recall: “I said to myself, as we proceeded through the day [of 9/11], ‘It’s working.’ All those days of patriotic duty were coming back and they were working.” According to ABC News, “If executive branch leaders and large numbers of congressmen had been killed in an attack on the United States, the plan could have gone further, officials suggest, perhaps even with non-elected leaders of the United States taking control and declaring martial law.” [ABC News, 4/25/2004] According to a White House timeline of the events of 9/11, it is in fact Cheney that “orders implementation of Continuity of Government and Continuity of Operations procedures,” at 9:55 a.m., although, according to the Washington Post, Cheney only “officially implemented the emergency Continuity of Government orders,” rather than activating the plan. [White House, 2001; Washington Post, 1/27/2002]
Between 9:45 a.m. and 9:56 a.m. September 11, 2001: Counterterrorism ‘Tsar’ Clarke Informed that President Bush Has Issued Shootdown Order, Earlier than Claimed by 9/11 Commission
According to his own account, counterterrorism “tsar” Richard Clarke is informed that President Bush has authorized the military to shoot down threatening aircraft. Clarke had requested that this authorization be given at around 9:36 (see (Between 9:30 a.m. and 9:37 a.m.) September 11, 2001). In his 2004 book Against all Enemies he will state that he receives a response shortly after the time people begin rapidly evacuating from the White House, and while Air Force One is getting ready to take off. This would therefore be sometime between 9:45 and 9:56. He gets a phone call from the Presidential Emergency Operations Center (PEOC) below the White House, where Vice President Dick Cheney and National Security Adviser Condoleezza Rice are located. On the other end is Army Major Mike Fenzel. Fenzel tells Clarke: “Air Force One is getting ready to take off, with some press still on board. He’ll divert to an air base. Fighter escort is authorized. And… tell the Pentagon they have authority from the president to shoot down hostile aircraft, repeat, they have authority to shoot down hostile aircraft.” Clarke replies, “Roger that.” In his recollection of this call, Clarke comments, “I was amazed at the speed of the decisions coming from Cheney and, through him, from Bush.” Clarke then gets the attention of those on the video conference screen for the Pentagon, and informs them, “the president has ordered the use of force against aircraft deemed to be hostile.” [CNN, 9/12/2001; Clarke, 2004, pp. 7-8] This description contradicts several other accounts of when the president gives the shootdown authorization. In late 2003, Clarke tells ABC News he gets the go-ahead from the vice president “within two minutes” after he requested shootdown authorization, meaning therefore around 9:37-9:38 (see (9:38 a.m.) September 11, 2001). [ABC News, 11/29/2003] Some accounts say that Bush gives the authorization later, at shortly after 9:56 (see (Shortly After 9:56 a.m.) September 11, 2001). [Sammon, 2002, pp. 102; Washington Post, 1/27/2002] According to the 9/11 Commission, it is not given until around 10:18 (see 10:18 a.m.-10:20 a.m. September 11, 2001). [9/11 Commission, 7/24/2004, pp. 41]
9:45 a.m.-9:56 a.m. September 11, 2001: Vice President Cheney Tells President Bush to Stay Away from Washington
Shortly after boarding Air Force One, President Bush speaks by phone with Vice President Dick Cheney for approximately 10 minutes. [Hayes, 2007, pp. 335-336] According to the 9/11 Commission, Cheney had reached the underground tunnel leading to the Presidential Emergency Operations Center (PEOC) below the White House at 9:37 a.m. (see (9:37 a.m.) September 11, 2001). He and the Secret Service agents escorting him had paused in an area of the tunnel with a secure phone and a television. He’d then asked to speak to the president, but it had taken a while for his call to be connected. However, elsewhere in its final report, the Commission will indicate that Bush, not Cheney, makes this phone call, saying that after he’d boarded Air Force One, the president “called the vice president.” [9/11 Commission, 7/24/2004, pp. 39-40] Cheney will later recall making “one phone call [to the president] from the tunnel. And basically I called to let him know that we [at the White House] were a target and I strongly urged him not to return to Washington right away, that he delay his return until we could find out what the hell was going on.” [Newsweek, 12/30/2001; 9/11 Commission, 7/24/2004, pp. 464] He will recall, “What I was immediately thinking about was sort of continuity of government.” [Hayes, 2007, pp. 335-336] According to notes made by White House press secretary Ari Fleischer, who is with the president on Air Force One, at about 9:45 a.m. Bush tells Cheney: “Sounds like we have a minor war going on here, I heard about the Pentagon. We’re at war… somebody’s going to pay.” [9/11 Commission, 7/24/2004, pp. 39 and 463; Fleischer, 2005, pp. 141] Bush instructs Cheney to call the congressional leadership and give them a briefing. [New Yorker, 9/25/2001] (However, around this time, Capitol Hill is being evacuated (see 9:48 a.m. September 11, 2001).) The 9/11 Commission will state that, according to “contemporaneous notes,” at 9:55 a.m. “the vice president [is] still on the phone with the president advising that three planes [are] missing and one had hit the Pentagon.” [9/11 Commission, 7/24/2004, pp. 40] In his book Against All Enemies, counterterrorism “tsar” Richard Clarke will indicate that it is around the time this call occurs that he is informed that the president has authorized the military to shoot down hostile aircraft (see (Between 9:45 a.m. and 9:56 a.m.) September 11, 2001). [Clarke, 2004, pp. 8] Yet various accounts of Bush and Cheney’s call will make no mention of the president and vice president discussing any orders or making any decisions. [Sammon, 2002, pp. 101; Woodward, 2002, pp. 16; 9/11 Commission, 7/24/2004, pp. 39-40; Hayes, 2007, pp. 335-336] Their call apparently ends around 9:56 a.m.-9:57 a.m., as, according to the 9/11 Commission, Cheney enters the PEOC “shortly before 10:00, perhaps at 9:58.” [9/11 Commission, 7/24/2004, pp. 40] (However, some accounts will indicate that he enters the PEOC significantly earlier than this (see (Shortly After 9:03 a.m.) September 11, 2001).) After hanging up, Bush turns to the men who are with him at his desk: his chief of staff Andrew Card, his senior adviser Karl Rove, military aide Lieutenant Colonel Tom Gould, and Fleischer. He tells them: “That’s what we’re paid for, boys. We’re gonna take care of this. When we find out who did this, they’re not gonna like me as president. Somebody’s going to pay.” [Sammon, 2002, pp. 101; Woodward, 2002, pp. 17] According to some accounts, shortly after finishing this call, the president and vice president will be back on the phone with each other (see (Shortly After 9:56 a.m.) September 11, 2001 and (Between 10:00 a.m. and 10:15 a.m.) September 11, 2001).
9:45 a.m. September 11, 2001: Lynne Cheney Arrives at the White House, but Guards Try to Stop Her Car Entering the Grounds
Lynne Cheney, the wife of Vice President Dick Cheney, arrives at the gate of the White House, but guards initially try to prevent her car from entering the grounds. [Newsweek, 12/30/2001; Milwaukee Journal Sentinel, 7/2/2002; Hayes, 2007, pp. 334] Cheney learned of the plane crashes at the World Trade Center while she was at a hair salon in Washington, DC (see (8:48 a.m.-9:03 a.m.) September 11, 2001), but her Secret Service agents only evacuated her from there after they learned an unidentified aircraft was flying toward the White House (see (Shortly After 9:33 a.m.) September 11, 2001). After initially driving toward the vice president’s residence, the agents changed direction to instead take Cheney to the White House. [United States Secret Service, 10/1/2001; White House, 11/9/2001] The White House is being evacuated when Cheney’s car arrives at its gate. [Newsweek, 12/30/2001] (It begins evacuating at around 9:45 a.m. (see (9:45 a.m.) September 11, 2001). [Associated Press, 2001 
; CNN, 9/12/2001] ) Cheney will later describe: “This was not the scene I’ve seen on camera, where people are now starting to run or anything.… [P]eople were all going in the other direction [to us] in a rather calm way when I arrived.” However, the guards at the gate will not let Cheney’s car enter the grounds. Cheney will say they have “no idea who we [are] and [are] confused that somebody would want to be coming in” when everybody else is leaving. Cheney’s driver takes the car over the curb and onto the sidewalk, to try and get Cheney to the White House, but a fire engine is driven in front of the car, to block its path. Eventually, though, Cheney’s car is allowed onto the grounds. [White House, 11/9/2001; Milwaukee Journal Sentinel, 7/2/2002; Hayes, 2007, pp. 334] Cheney will enter the White House at 9:52 a.m. (see 9:52 a.m. September 11, 2001). [United States Secret Service, 11/17/2001 ; 9/11 Commission, 7/24/2004, pp. 40]
9:45 a.m. September 11, 2001: United Airlines Orders Its Flights to Land
United Airlines orders all its flights to land at the nearest airport. Andy Studdert, the airline’s chief operating officer, will tell the 9/11 Commission, “At approximately 9:45 I order the entire United fleet grounded, for the first time in United history.” He will add, “Even before this, some individual dispatchers were already grounding their flights.” [9/11 Commission, 1/27/2004] Studdert gives the instruction, “Tell them to get to the nearest airport they can.” [USA Today, 8/12/2002] The FAA gives out a similar order to all its facilities around this time (see (9:45 a.m.) September 11, 2001). [9/11 Commission, 7/24/2004, pp. 29] American Airlines ordered its aircraft to land earlier on, at around 9:15 (see (9:15 a.m.) September 11, 2001). [9/11 Commission, 8/26/2004, pp. 31] United Airlines has already ordered a ground stop, preventing any new takeoffs of its aircraft (see (9:20 a.m.) September 11, 2001). [Wall Street Journal, 10/15/2001; 9/11 Commission, 7/24/2004, pp. 10]
9:45 a.m. September 11, 2001: Airborne Operations Center Launches from Base near Washington
An E-4B National Airborne Operations Center, with the call sign “Venus 77,” takes off from Andrews Air Force Base, near Washington, DC, in response to the attack on the Pentagon. [Federal Aviation Administration, 9/11/2001 ; 9/11 Commission, 2/17/2004; Farmer, 2009, pp. 206] The E-4B is a highly modified Boeing 747, fitted with sophisticated communications equipment, which can serve as a flying military command post during a national emergency. The US military has four of these planes. [Federation of American Scientists, 4/23/2000; Dayton Daily News, 9/12/2001; Verton, 2003, pp. 143] Venus 77 takes off at 9:43 a.m., according to John Farmer, who will be senior counsel to the 9/11 Commission. [Farmer, 2009, pp. 206] But the flight tracking strip from Andrews Air Force Base will record it as having taken off at 9:45 a.m. [Federal Aviation Administration, 9/11/2001 ; 9/11 Commission, 2/17/2004] The plane is initially directed toward Offutt Air Force Base in Nebraska. But shortly after taking off, its pilot tells air traffic control that he wants to fly to Wright-Patterson Air Force Base in Ohio. [Farmer, 2009, pp. 206] Wright-Patterson is one of the few designated bases for the E-4B. Another E-4B has actually been on the ground there and takes off around this time (see Shortly After 9:37 a.m. September 11, 2001). [Dayton Daily News, 9/12/2001] The pilot of Venus 77 is cleared to head to Wright-Patterson and so he turns west. But he then says he wants to turn back east and hold south of Washington. He will be cleared to do so at 9:47 a.m. and his plane will eventually settle into a holding pattern over Richmond, Virginia. [Farmer, 2009, pp. 206-207] Farmer will claim that Venus 77 is the “mystery plane”—an unidentified white aircraft—seen over Washington around this time (see (9:41 a.m.-9:42 a.m.) September 11, 2001). [Farmer, 2009, pp. 372] However, that plane was reported to be “circling the White House” at 9:41 a.m., before Venus 77 takes off. [ABC News, 9/11/2001] Another E-4B, with the call sign “Word 31,” took off from Andrews Air Force Base at around 9:27 a.m. (see (9:27 a.m.) September 11, 2001), so that aircraft might be the “mystery plane” seen flying over Washington. [Federal Aviation Administration, 9/11/2001 ; Verton, 2003, pp. 143-144; 9/11 Commission, 2/17/2004]
9:45 a.m. September 11, 2001: Flight 93 Hijacker Asks for the ‘Pilot’ to Be Brought Back into the Cockpit
A hijacker in the cockpit of Flight 93 asks another hijacker if they should “let the guys in” and that hijacker then suggests that they “bring the pilot back.” The cockpit voice recording from Flight 93 will later reveal that, speaking in Arabic, one of the hijackers says: “How about we let them in? We let the guys in now.” He then repeats his question, asking, “Should we let the guys in?” He is apparently suggesting that they allow the other hijackers on Flight 93 into the cockpit. The other hijacker in the cockpit replies, “Inform them and tell him to talk to the pilot.” He then says, “Bring the pilot back.” Journalist and author Tom McMillan will comment that this reference to the pilot “underscored the notion that [Ziad Jarrah, the hijacker believed to be at the controls of Flight 93] was overmatched by the Boeing 757” and is also “apparent confirmation that at least one of the United pilots—either Captain [Jason] Dahl or First Officer [LeRoy] Homer—was still alive, and likely in the first-class cabin.” [Federal Bureau of Investigation, 12/4/2003; McMillan, 2014, pp. 96] However, at around this time, passenger Todd Beamer reports in a call from Flight 93 that the plane’s captain and first officer are lying on the floor of the first-class cabin, and are injured or possibly dead (see 9:45 a.m.-9:58 a.m. September 11, 2001). [Longman, 2002, pp. 199; 9/11 Commission, 8/26/2004, pp. 43] Indeed, McMillan will note that “[n]o one ever was brought to the cockpit to assist with the aircraft’s operation and the hijackers never mentioned ‘the pilot’ again” on the cockpit voice recording. One of the hijackers in the cockpit, still speaking in Arabic, then whispers: “In the name of Allah. In the name of Allah. I bear witness that there is no other God but Allah.” Less than 30 seconds later, at 9:46 a.m., the cockpit voice recorder will pick up the sound of two knocks on the cockpit door followed by the sound of the door opening. A couple of minutes after that, the recorder will pick up the sound of “distinctive knocks” on the cockpit door, again followed by the sound of the door opening. What exactly is happening on these occasions is unknown. [Federal Bureau of Investigation, 12/4/2003; McMillan, 2014, pp. 96]
9:45 a.m.-10:45 a.m. September 11, 2001: Witnesses First Notice Military Jets over New York, Later than Claimed in 9/11 Commission’s Account
According to the accounts of numerous witnesses on the ground near the World Trade Center, military fighter jets are first noticed flying over Manhattan either shortly before or soon after the second collapse, at 10:28 a.m. Some witnesses recall fighters arriving just before this collapse: 
Emergency medical technicians Dulce McCorvey and Michael D’Angelo hear fighters flying over Manhattan at unspecified times after the first tower’s collapse. [City of New York, 10/3/2001; City of New York, 10/24/2001] Fire Lieutenant Sean O’Malley and firefighters Pete Giudetti and Dan Potter notice jet fighters flying overhead soon before the second collapse. [City of New York, 10/12/2001; City of New York, 12/6/2001; Smith, 2002, pp. 49-50]
Other witnesses say the fighters arrive soon after this collapse: Deputy Fire Chief Robert Browne, police officer Peter Moog, and emergency medical technicians Richard Zarrillo and Jason Katz notice fighters overhead immediately after, or fairly soon after, the second tower’s collapse. [City of New York, 10/24/2001; City of New York, 10/25/2001; City of New York, 12/20/2001; Fink and Mathias, 2002, pp. 79-80] Mayor Rudolph Giuliani, Police Commissioner Bernard Kerik, and Office of Emergency Management Director Richard Sheirer are heading north together after leaving their temporary command post on Barclay Street (see (9:50 a.m.-10:10 a.m.) September 11, 2001). In some accounts, all three of them recollect hearing the first military jets overhead soon after the second tower’s collapse. [Kerik, 2001, pp. 339-340; Giuliani, 2002, pp. 14; 9/11 Commission, 5/18/2004 ] However, according to another account, Giuliani hears the first jet slightly earlier, at around 10:20 a.m. And, in his private testimony before the 9/11 Commission, Kerik claims to have heard a fighter jet coming when he was heading to the temporary command post on Barclay Street, i.e. shortly before 9:50 a.m. [Barrett and Collins, 2006, pp. 348-349]
A few witnesses claim the fighters arrive earlier on, before the first collapse at 9:59 a.m.: Emergency medical technician Frank Puma and Port Authority Freedom of Information Administrator Cathy Pavelec say they see fighter jets overhead at unspecified times before the first collapse. [City of New York, 12/12/2001; Fink and Mathias, 2002, pp. 68]
The fighter(s) are presumably the F-15s launched from Otis Air Force Base at 8:46 a.m. (see 8:46 a.m. September 11, 2001). However, the 9/11 Commission will claim that these arrived over Manhattan at 9:25 a.m. (see 9:25 a.m. September 11, 2001), which is significantly earlier than most of the witnesses on the ground recall.
9:45 a.m. September 11, 2001: National Security Adviser Rice Heads to White House Bunker on Orders of the Secret Service
National Security Adviser Condoleezza Rice is escorted toward the Presidential Emergency Operations Center (PEOC), the bunker below the White House, by Carl Truscott, the Secret Service special agent in charge of the presidential protective division. [United States Secret Service, 10/1/2001; White House, 11/1/2001; Felix, 2002, pp. 227] Rice was in the White House Situation Room when the Pentagon was hit at 9:37 a.m., according to her own later recollections, and had subsequently looked up and seen the television footage of the burning building. [White House, 11/1/2001; Bumiller, 2007, pp. xiii]
Rice Told She Must Go to the PEOC – “[T]he picture had just come up on television of the plane lodged in the side of the Pentagon,” Rice will recall. “And no one had told me. I literally turned and looked at the picture and saw it.” She will say: “And then there were incoming reports that there had been a car bomb at the State Department, that there was a large fire on the Mall near the Washington Monument, and [I was] just trying to sort through the information when a Secret Service agent [i.e. Truscott] came and said: ‘You have to go to the bunker. The vice president is already there. There may be planes heading for the White House.’” [MSNBC, 9/11/2002] Rice will say Truscott is “quite firm” when he talks to her. [White House, 8/7/2002]
Secret Service Agent Is Heading to the PEOC from Nearby Building – Truscott has just come from his office in the Eisenhower Executive Office Building, next to the White House, where he was meeting with other Secret Service agents to discuss security matters. One issue the agents discussed was providing protection for Rice (see (9:18 a.m.) September 11, 2001). During the meeting, Truscott learned that a suspicious aircraft was flying toward Washington, DC (see (Shortly After 9:35 a.m.) September 11, 2001), and instructed a “security representative” to evacuate the White House. He then left his office and headed toward the PEOC, meeting Rice on his way there. [United States Secret Service, 10/1/2001]
Rice Is ‘Pushed Along’ toward the PEOC – Rice briefly talks on the phone with President Bush and warns him not to return to Washington before she leaves the Situation Room (see (9:45 a.m.) September 11, 2001). [Felix, 2002, pp. 227; White House, 8/2/2002; White House, 8/6/2002] She is then escorted down toward the PEOC. [White House, 11/1/2001] She will recall being “pushed along” the corridors by Truscott as she heads there. [White House, 8/2/2002] Truscott and Rice will encounter Vice President Dick Cheney and his wife, Lynne Cheney, in the underground tunnel leading to the PEOC, and then enter the PEOC shortly before 10:00 a.m. (see (Shortly Before 9:59 a.m.) September 11, 2001). [United States Secret Service, 10/1/2001; Bumiller, 2007, pp. xiii] White House counterterrorism chief Richard Clarke will contradict Rice’s account, however, indicating that Rice headed to the PEOC significantly earlier, roughly around 9:15 a.m. (see (9:15 a.m.) September 11, 2001). [Clarke, 2004, pp. 3-4]
9:45 a.m.-9:53 a.m. September 11, 2001: Passengers Are Subjected to a Strict Security Check while Boarding Air Force One
Secret Service agents subject reporters and other individuals who are traveling with President Bush to a strict security check as they are getting onto Air Force One. Bush’s motorcade has now arrived at Sarasota-Bradenton International Airport in Florida, where Air Force One is waiting (see (9:43 a.m.) September 11, 2001). [Sammon, 2002, pp. 99; Rochester Review, 9/2004] The plane’s crew members have been told there is a “great potential that we are going to be under attack sitting on the ramp” at the airport, according to Colonel Mark Tillman, the pilot. They have also been told there are “unidentified people all around the airport,” and that there is a “possibility that we were subject to the plan to go ahead and assassinate the president” (see (9:04 a.m.-9:55 a.m.) September 11, 2001). [United Services Automobile Association, 9/11/2011] Reporters who are heading for the rear entrance to Air Force One are stopped by Secret Service agents and ordered to drop whatever they are carrying for a security sweep. [Sammon, 2002, pp. 99] One reporter, White House correspondent Richard Keil, will later recall seeing “a dozen additional Secret Service agents” at the airport, “each with bomb-sniffing dogs.” “We usually have our bags inspected only once in the morning, as long as we remain inside the secure ‘bubble’ in which the president travels,” Keil will write. But now, “everyone’s bag had to be re-swept.” [Rochester Review, 9/2004] Even staffers who are wearing special lapel pins showing they are White House employees have their belongings checked by the bomb-sniffing dogs. [Sammon, 2002, pp. 99] Passengers also have to confirm who they are before being allowed onto the plane. “There was a lot of attention to our credentials, who we were,” Sandy Kress, Bush’s senior education adviser, will comment, adding: “We had to show ID and our badge, not just the badge. And this even though the crew knew most of us.” [Politico Magazine, 9/9/2016] Meanwhile, a military aide standing at the foot of the rear entrance to the plane snaps: “If you’re not essential, you’re not getting on the airplane! We gotta hurry up and get out of here.” [Sammon, 2002, pp. 99] Tillman will recall that Secret Service agents and the plane’s own security staffers are “double, triple-checking the manifest,” and the bomb-sniffing dogs “search everything” that comes onto Air Force One. “We didn’t want to take any chances,” he will comment. [United Services Automobile Association, 9/11/2011; US Air Force, 2/29/2012 ] The mood, according to journalist and author Bill Sammon, is “extraordinarily tense.” [Sammon, 2002, pp. 99]
