By Gordon Corera
BBC Security correspondent
The reform of America's intelligence services has been a hard-fought struggle, but serious questions are now being asked: exactly how will this new structure work in practice, and will it really improve the ability of the US to defend itself?
One of the central findings of the 9/11 Commission was the lack of co-operation and communication within the country's vast intelligence community.
Intelligence reform has provoked fierce debate in Congress
It is a community which contains 15 agencies, 200,000 employees and costs an estimated $40bn a year.
But it has found it hard to communicate, share information and set common priorities.
It has also struggled to integrate foreign and domestic information - something which is vital in fighting terrorists who cross borders.
"I think one reason that we missed some of the issues, be it Iraq or 9/11 was that we didn't have a truly focused, truly centralised and truly efficient intelligence-collection approach to the problems we face," John MacGaffin, a former senior CIA and FBI official told the BBC.
At the heart of the reforms is the creation of a new position of National Intelligence Director.
Until now a single individual, the Director of Central Intelligence (DCI), has had a series of overlapping responsibilities in leading America's intelligence community.
The Iraq inquiries made clear that the failure was not one of structure but of not having enough spies on the ground
The DCI has been the Director of the CIA, has managed the overall intelligence community and acted as the president's chief intelligence adviser.
The 9/11 Commission - along with many previous studies - stated that "no recent DCI has been able to do all three effectively".
Porter Goss, the recently installed head of the CIA, will see parts of his job hived off so that he only runs the human spy agency and the CIA will lose its position as first among equals in the US intelligence community.
The new National Intelligence Director will become the co-ordinator of the whole community, advising the president and bringing information together.
US INTELLIGENCE BILL
Establishes director of national intelligence
Creates a national counter-terrorism centre
Sets up a civil liberties board
Increases border patrols
Tightens visa requirements
Strengthens rights to investigate terror suspects
It is the co-ordinating role which is the most unclear and the reason that reform very nearly didn't happen.
At the moment, the Pentagon actually controls more than 80% of the intelligence budget.
The most expensive part of the spying game is not the CIA - which runs human spies - but bodies like the National Security Agency, which runs America's eavesdropping capability, or the National Reconnaissance Office and National Geo-Spatial Intelligence Agency, which collect mapping, imagery and satellite reconnaissance.
The Pentagon has long argued that these agencies are vital to supporting troops in combat.
Getting quick access to satellite images of a war zone or listening in to your enemy's communications is increasingly important in the modern battlefield.
The military argued that if they lost control over these agencies then they might lose some of their ability to protect troops in combat.
Someone, somewhere, has to decide priorities and whether a satellite passing over the Middle East looks at possible nuclear sites in Iran or at the movements of insurgents in Iraq.
The battle was over who would do that.
The Pentagon's allies in Congress fought long and hard against losing control and in the end gained assurances that the chain of command would not be broken and the military would not find itself losing out.
So exactly how much control will the new director really have?
The devil will be in the detail: exactly how will authority will be divided in practice between the new director and the Pentagon?
New CIA director Porter Goss will see his powers trimmed
Can the new official really set tasking across all the different agencies, or will he instead become an impotent figure, setting priorities but without the budgetary clout to force people to carry them out?
Others also ask whether it is dangerous to create a director figure who does not have his own institution like the CIA behind him.
Could he end up a floating manager without real institutional clout who is too distant from the people in the field doing their job?
21st century intelligence
The next question is how much energy the process of re-organising consumes. One parallel may be with the Department of Homeland Security, where multiple agencies were pulled together but have taken a long time to adapt and learn to work together.
Some fear that a similar upheaval might distract the intelligence community from its day-to-day work.
And the last major question is how much difference, broad institutional re-organisation will really mean to people on the ground.
The CIA will lose its position as 'first among equals'
The inquiries into problems over Iraq's weapons of mass destruction made clear that the failure was not one of the wrong structure but one of not having enough spies on the ground and not analysing the intelligence in a sufficiently balanced way.
These are problems that Porter Goss, the new chief of the CIA, is trying to address, but which are quite independent of the reforms that Congress has been passing.
Before this week America's intelligence structure had barely changed since the start of the Cold War.
Reformers hope that the new structure will be one capable of dealing with the very different trans-national threats of the 21st century.
But it may take some time before it is clear just how much difference reform has really made.