By Adam Brookes
BBC correspondent in Washington
James Pavitt, the Director of Operations, announced he was retiring on Friday.
Some see a fresh start at the CIA with the departure of George Tenet
The announcement came just a day after the CIA's Director George Tenet said he was stepping down, but an agency spokesman says the two departures are not related.
Mr Pavitt's job is an extraordinarily sensitive one.
He is responsible for running the case officers, agents and paramilitaries that make up the agency's clandestine service.
The agency says his and George Tenet's departures are simply two retirements, not a leadership crisis.
Nonetheless sources close to the intelligence agencies say that with Mr Tenet and Mr Pavitt gone, the CIA can make a fresh start after the body blow to its credibility that was the failure to find weapons of mass destruction in Iraq.
And there's a political upside for President George W Bush, too.
"With George and James resigned," said one source, "Donald (Rumsfeld) and Condi (Rice) will feel like they don't have to."
The spies' difficult summer
America's intelligence community - 14 agencies, tens of thousands of personnel, billions in budget - is in for a difficult time this summer.
Born 5 January 1953 in New York to Greek immigrants
Studied at Georgetown and Columbia universities
Served on Clinton's National Security Council 1992-95
Deputy CIA director 1995-96
Acting CIA director 1996-97
Confirmed as CIA director 1997
Reports from the Senate and from an independent commission will dissect the spies' successes and failures role in the fight against terrorist organizations and in the lead up to the war in Iraq.
The reports are likely to be very critical of the organization and culture that prevails in the secret corridors.
They will probably recommend restructuring of parts of the intelligence community to guarantee better intelligence sharing among agencies and a less confused command structure.
Currently, the CIA - the lead intelligence agency - takes its direction from the National Security Council and the State Department.
But other agencies, notably the massive National Security Agency, answer to the Pentagon. The FBI comes under the Department of Justice.
Intelligence reform could include the creation of a single intelligence overseer with real executive authority.
One source told the BBC that the administration may try to pre-empt the reports by announcing some kind of intelligence reform before the end of July.
"Watch for the White House to move on this before the 9/11 Commission publishes its report", the source said.
Choices for CIA chief
A new CIA director will want to let those controversies die down before he takes over.
That means it's unlikely we'll see a new, permanent Director of Central Intelligence until after the presidential elections in November.
Nonetheless, Washington on Friday was abuzz with speculation over who might succeed George Tenet as Director of Central Intelligence.
The top candidate to take over the CIA is Porter Goss.
He's a Republican congressman and chairman of the House Intelligence committee.
Mr Goss used to be an intelligence officer himself and is well acquainted with the byways of legislation and politics.
But another contender may be Richard Armitage.
Mr Armitage, a former naval officer known for his weightlifting abilities and his fluent Vietnamese, is currently Deputy Secretary of State.
In the frequent tussles between the State Department and Department of Defence, he's seen as a close ally of Colin Powell, and an antagonist of the 'neocons' - hardliners in the Pentagon who are suspicious of diplomatic engagement as a means of projecting American power.
Sources close to the intelligence community say Mr Armitage is known to want the CIA job.
But if President Bush were to give it to him, it may well be seen as a rebuke to the Pentagon.
Such a show of political disunity wouldn't do the administration any good.