I am looking for a link to the full text of an article that appeared
in either a major newspaper (NY Times, Wash. Post, Baltimore Sun) or
one of the weekly news magazines in the two months following last year's
September 11th attacks. The article outlined a timeline of  the
federal government's response to the attacks within the first 48
hours, specifically focused on the President.

The specific article that I am looking for has a quote from one of the
Congressional leaders who was describing discussions immediately after
the attacks.  The executive branch wanted congressional leaders to
evacuate on helicopters.  Some leaders in congress wanted to stay in
session.  The specific quote that I am looking for has a leader of
Congress saying that the two branches of government were seperate and
that the executive branch couldn't determine if Congress would remain
in session or not.  The response from one representative of the
executive branch was something along the line of, "That's true, but
today we control the helicopters."

Hello.

The article is:

"America's Chaotic Road to War: Bush's Global Strategy Began to Take
Shape in First Frantic Hours After Attack" by Dan Balz and Bob
Woodward
Washington Post, Sunday, January 27, 2002; Page A01

For full-text visit the web site of the Washington Post:
http://www.washingtonpost.com/ac2/wp-dyn/A42754-2002Jan26?language=printer

Here is an excerpt from the article that includes the exact discussion
that you mention:

"The leaders agitated to get out of their bunker and back to
Washington, but Cheney resisted. Terrorist threats persisted and there
was no way to guarantee their security, he said. Sen. Don Nickles
(R-Okla.) protested. We're a separate branch of government-why do we
need the approval of the White House, he complained.
'Don,' the vice president replied, 'we control the helicopters.'"

search strategy: "we control the helicopters"

I hope this helps.

Absolutely perfect.  Not sure why I couldn't find it.  Thank you so much.