U.S. intelligence officials are trying to assess what the protests in Egypt will mean for the partnership between the two countries.
The United States and Egypt work closely on a range of intelligence issues — especially terrorism.
Before it can look ahead, though, the spy community is being asked some hard questions about whether it missed the signals that Egyptian President Hosni Mubarak's regime was in jeopardy.
Secrets And Mysteries
There's a sense in Washington that the Egyptian uprising just came out of nowhere.
"It has taken not just us but many people by surprise," Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, said on The Daily Show.
Some senators on Capitol Hill have started looking around for someone to blame. During an intelligence committee hearing this week, California Democrat Dianne Feinstein questioned whether the U.S. intelligence community should have been able to predict the Egyptian revolt.
The witness at the hearing was Stephanie O'Sullivan, who has been tapped to be the country's No. 2 intelligence officer.
At one point, Sen. Ron Wyden of Oregon asked her a direction question: "When did the intelligence community first alert the president and policymakers that protesters were likely to threaten President Mubarak's hold on power?"
"We have warned of instability," O'Sullivan answered. "We didn't know what the triggering mechanism would be."
Predicting the "triggering mechanism" is often the problem, says Gen. Michael Hayden, former head of the CIA. Hayden says political volatility in Egypt has been tracked for years. But there are limits to what spies can know.
To explain this, he borrows from what a CIA colleague, John McLaughlin, likes to say: There's a difference between secrets and mysteries.
"He said you can't hold intelligence services accountable in the same way for mysteries," Hayden says. "The broad movement of Egyptian society isn't a secret that was hidden in somebody's safe that somebody should have expected us to purloin. This is far more difficult to understand."
Cooperation In The Future?
What's also difficult to understand at this point is how the Egyptian uprising will affect the way U.S. and Egyptian spy agencies will continue to work together.
Omar Suleiman, Egypt's former intelligence chief and now its vice president, has been one of America's closest partners.
"We have a saying at the agency when we have a very good friend: 'We have a lot of time for him.' We always had a lot of time for Director Suleiman," Hayden says.
The relationship between the two spy agencies has been close. But it hasn't been without controversy. For example, there's the CIA program known as extraordinary rendition, in which suspects with links to al-Qaida were apprehended and flown to third-party countries, like Egypt.
Tom Malinowski of Human Rights Watch has studied extraordinary rendition. "Obviously, the Americans knew what was going to happen to people who were rendered to Egypt," he says. "Why send someone to Egypt if not for the purpose of having them interrogated in the Egyptian manner?"
U.S. officials have denied sending any detainees to countries where they may have been tortured.
Former U.S. intelligence officials say the Mubarak regime has been a key ally on Iran, Israel and the Palestinians, and Hezbollah in Lebanon.
Hayden says Egypt and the U.S. will always find ways to cooperate on intelligence matters when it's in their interests. But, he says, "to the degree the new government adopts policies that might be different than the policies of the Mubarak government, that could make the intelligence relationship less productive for both nations."
And as for who leads Egypt next? That may be another one of those mysteries the CIA can't solve.