The Official Account
Vice President Dick Cheney took charge of the government’s response to the 9/11 attacks after he entered the PEOC (the Presidential Emergency Operations Center), a.k.a. “the bunker.”
The The 9/11 Commission Report said  that Cheney did not enter the PEOC until almost 10:00 AM, which was at least 20 minutes after the violent event at the Pentagon that killed more than 100 people.
The Best Evidence
Secretary of Transportation Norman Mineta told the 9/11 Commission that, after he joined Cheney and others in the bunker at approximately 9:20 AM, he listened to an ongoing conversation between Cheney and a young man, which took place when “the airplane was coming into the Pentagon.” 
After the young man, having reported for the third time that the plane was coming closer, asked whether “the orders still stand,” Cheney emphatically said they did. The The 9/11 Commission Report, by claiming that Cheney did not enter the PEOC until long after the Pentagon was damaged, implies that this exchange between Cheney and the young man — which can most naturally be understood as Cheney’s confirmation of a stand-down order — could not have occurred.
However, testimony that Cheney was in the PEOC by 9:20 was reported not only by Mineta but also by Richard Clarke  and White House photographer David Bohrer.  Cheney himself, speaking on “Meet the Press” five days after 9/11, reported that he had entered the PEOC before the Pentagon was damaged. 
The 9/11 Commission’s attempt to bury the exchange between Cheney and the young man confirms the importance of Mineta’s report of this conversation.
References for Military Commands Point 3
- The 9/11 Commission Report (2004), note 213, p. 464 (pdf-p. 481).
- “911 Commission: Trans. Sec. Norman Mineta Testimony” (YouTube: derdy).
- Richard Clarke, “Against All Enemies: Inside America’s War on Terror” (New York: Free Press, 2004), pp. 2-5.
- See “9/11: Interviews by Peter Jennings,” ABC News, September 11, 2002.
- “The Vice President Appears on Meet the Press with Tim Russert,” MSNBC, September 16, 2001.