>> Tonight on Frontline... (explosion) ...another terrorist attack.

>>We need help!

>> And new questions about whether Americans are safe... >>Two explosions near the finish line just a short while ago.

>> Since 9/11, the government has been building a huge anti-terror apparatus... >>What happens after 9/11 is this tremendous ramping up.

>>The money just came out of Congress.

It was flying out.

>> Pulitzer Prize-winning journalist Dana Priest traces America's journey from 9/11 to the Boston Marathon bombing.

>>It's shrouded in secrecy.

>> Tonight on Frontline: "Top Secret America: 9/11 to the Boston Bombings."

>>Good morning, America.

I'm Charles Gibson.

>>I'm Diane Sawyer, and it's Tuesday, September 11, 2001.

(people screaming) >>Just a few moments ago, something believed to be a plane crashed into the south tower of the World Trade Center.

>>A plane has crashed into one of the towers.

>>It looks almost like a mushroom cloud.

>>We're trying to figure out exactly what happened, but clearly something relatively devastating.

>>Welcome back to Fox News.

We have a very tragic alert for you right now.

>>Something hit the Pentagon on the outside of the fifth floor.

>>A day unlike any other in the long course of American history: a terrorist act of war against this country.

President Bush saying toda that freedom has been attacked by... >>BUSH: Make no mistake, the United States will hunt down and punish those responsible for these cowardly acts.

>>CLARKE: President Bush said to us in the basement of the White House on the night of 9/11, "You have everything you need."

And that was true because, as soon as we went to the Congress, they said, "Just tell us what you need."

Blank check.

>>NARRATOR: The President was determined to spend whatever was necessary and do whatever was necessar to conduct a new kind of war.

>>ASHCROFT: The President turned to me and said-- in my direction anyhow-- he said, "Never let this happen again."

>>TOWNSEND: I understood that to mean there was no end of the earth we weren't willing to go to, there was nothing we weren't willing to ask for, there was nobody we wouldn't work with.

>>NARRATOR: The key to the new war would be secrecy.

>>CHENEY: We'd have to work the dark side, if you will.

We've got to spend time in the shadows in the intelligence world.

>>PRIEST: In the first few days, the entire blueprint for what would happen over the next decade was written, all in secret.

The public didn't know, the media didn't know, and it would take us years to find out.

>>NARRATOR: For ten years, Pulitzer Prize-winning reporter Dana Priest has reported on hidden military and intelligence operations.

>>CHENEY: A lot of what needs to be done here will have to be done quietly, without any discussion, using sources and methods that are available to our intelligence agencies.

>>PRIEST: In the beginning, we saw a little bit of this world everywhere, and we were gathering bit by bit.

>>CHENEY: It's going to be vital for us to use any means at our disposal to achieve our objective.

>>PRIEST: It really took years to figure out how big it really was, and we were shocked.

>>NARRATOR: For Priest, one of the first hints of the secret war was revealed at this Congressional hearing.

>>SENATOR: The joint inquiry hearing will come to order, please.

>>BLACK: When I speak, I think the American people need to look into my face, and I want to look the American people in the eye.

My name is Cofer Black.

>>NARRATOR: Cofer Black was in charge of the CIA's counterterrorism efforts.

>>BLACK: This is a very highly classified area.

All you need to know is that there was a "before 9/11" and there was an "after 9/11."

After 9/11, the gloves come off.

>>NARRATOR: Beyond that, Black refused to divulge any details.

>>PRIEST: They just wanted no information out.

I think the reality is that they wanted to keep it secret because they were doing things that a lot of people would not approve of, and they wanted to do them as long as they could without being found out.

>>NARRATOR: The plan for the secret war began here at the Central Intelligence Agenc in the hours right after 9/11.

>>McLAUGHLIN: The reaction in our building and among our leadership was pretty simple: anger and resolve.

We were fighting these guys, and they won a huge victory on that day, and it was a huge defeat for us.

>>BLACK: This one has finally got past all of our defenses.

We had plans that had been developed in the past that had reached their due date with 9/11.

>>PRIEST: He was very aggressive.

He saw no boundaries to what he could do.

At one point, he talks about bringing bin Laden's head on a platter with flies on the eyeballs.

>>SCHROEN: When 9/11 happened, it was Cofer who really took the lead in... in being the most vocal person, saying, "Okay, this is a tragedy, "but the gloves are off.

"We're going to go out and we're going to defeat Al Qaeda, "we're going to kill bin Laden, and we're going to win this war."

>>NARRATOR: That night, they prepared an operational plan.

>>BRENNAN: Cofer and his people pulled together what was going to be the next step as far as going after Al Qaeda, going after Afghanistan.

And they were the ones that actually were able to bring the plans to the table first and present them at the White House.

>>BLACK: Where everybody else is looking for their maps on Afghanistan, we're ready to rock, ready to roll.

I mean, we were waiting for the bureaucracy to catch up.

>>NARRATOR: Black would personally present the plan to President Bush.

>>BRENNAN: CIA had already done more homework on Al Qaeda than any other part of the US government.

And so, what they were able to do then was to put together a proposal and a timeline as far as how the CIA could be the vanguard of the US government move against Al Qaeda.

>>NARRATOR: The CIA code name for the covert program would become "Greystone."

>>PRIEST: They had a matrix that they offered to the White House that said, "These are the countries we need to go into.

"Go after bin Laden and his terrorist network.

Kill and capture them and their supporters."

>>NARRATOR: Greystone was a challenge to the old ways of fighting, and the Secretary of Defense, Donald Rumsfeld, knew it.

>>PRIEST: So the CIA was very much in front of the military, and that bothered Rumsfeld greatly.

>>NARRATOR: But Rumsfeld's generals had no plans for dealing with Al Qaeda or Afghanistan.

>>DELONG: We had no plan.

I mean, to be honest, you have operational plans for different parts of the world.

There was none for Afghanistan.

>>NARRATOR: Rumsfeld scrambled, but Cofer Black was way ahead of him.

In less than a week, the President initiated Greystone.

>>McLAUGHLIN: We all assembled in the Cabinet Room, and the President lays down about 12 decisions, just like that, machine-gun fashion.

>>INTERVIEWER: What did he say?

>>McLAUGHLIN: Well, of course, the thing that stands out in my memory, because it hit me vividly, was... he said, "I want CIA in there first."

>>NARRATOR: That day, President Bush signed a key document, a finding authorizing Cofer Black and the CIA to wage a covert international war.

>>RADSAN: It was a very comprehensive finding.

It was generally worded.

It was: "Go out and get the bad guys; disrupt them, kill them, interrogate them."

This was an overarching authorization of the CIA.

>>RIZZO: I had never seen a presidential authorization as far reaching and as aggressive in scope.

It was... it was simply extraordinary.

>>TOWNSEND: In a post-9/11 world, we weren't going to be so prissy.

We were going to work and do what we needed to do.

No matter how difficult or undesirable it was, we were going to do what we needed to do to get the information we needed to protect the American people.

>>NARRATOR: The finding would set the ground rules for the new war on Al Qaeda.

>>PRIEST: That sets in motion the largest covert action program since the height of the Cold War, and many people inside the agency will sa it's even larger than that.

>>BLACK: Now, basically in a nanosecond, we're going from where we were staked to the ground like a junkyard dog-- you can report but you can't do anything-- to new authorities, new rules of engagement, lots of funding to support this.

This is a whole new ball game.

>>NARRATOR: Within two weeks in Afghanistan, the first phase of Greystone began.

>>SCHROEN: My team-- seven officers, including myself and three air crew-- flew in on the 26th of September.

When I began to distribute money-- $200,000 here, $250,000 for this-- I think the Afghans were convinced that we... we were sincere.

>>BLACK: The action was planned to be classic CIA.

It's going to be a multi-prong threat attack where we work with locals, minimize the American footprint.

>>BERNTSEN: CIA officers, of course, in Afghanistan for the first time since, you know, World War II, are involved in battlefields and combat operations, doing things that we hadn't done in 60 years.

So I think it's kind of a shock to the military.

>>PRIEST: The CIA went in right off the bat, hooked up with the Northern Alliance, and it was really quite remarkable what they accomplished with so few people on the ground.

(gunfire) >>NARRATOR: It didn't take long for the Taliban to fall.

The CIA had demonstrated it could fight effectively in the shadows.

(horn honking) >>BLACK: We'd like the survivors of 9/11 to know that those of us in the business consider it the CIA's finest hour.

We went in to kick ass, and we did.

(siren blaring) >>There have been dramatic developments on the ground in the war in Afghanistan.

>>The Taliban have suffered a series of defeats as Northern Alliance... >>NARRATOR: Washington publicly celebrated the first victor in what they began to call "the war on terror."

>>There were celebrations in Afghanistan's capital today.

>>The capture of Kabul follows a series of stunning successes by the Northern Alliance.

>>HOUSE SERGEANT AT ARMS: Mr. Speaker, the President of the United States!

(cheers and applause) >>BUSH: Terrorists who once occupied Afghanistan now occupy cells at Guantanamo Bay.

(cheers and applause) And this evening, we welcomed the distinguished interim leader of a liberated Afghanistan, Chairman Hamid Karzai.

(cheers and applause) >>PRIEST: The victory in Afghanistan came so quickly, and the ball kept rolling in secret.

And, by and large, it's continued in secret.

>>NARRATOR: Greystone was under wa well beyond the borders of Afghanistan.

In more than a dozen countries, operatives were fighting a global secret war.

>>DELONG: George Tenet calls me one morning and said, "We've got our target."

I said, "Okay, we're good, I'm going down to the UAV room."

>>NARRATOR: The Unmanned Aerial Vehicle room was in Tampa, Florida.

A drone was flying over Yemen.

The target was in an SUV.

>>I got a vehicle moving out.

>>Are the vehicles moving right now?

>>DELONG: I'm sitting back like this, looking at the wall and talking to George Tenet.

And he goes, "You going to make the call?"

And I said, "I'll make the call."

He says, "This SUV over here is the one that has Ali in it."

I said, "Okay, fine.

You know, shoot 'em."

>>You are clear to engage it.

>>DELONG: They lined it up and shot it.

>>Score.

Roll it in.

(gunfire) Oh!

>>Good shot.

>>DELONG: It's a pretty good- sized explosive.

In an SUV, you can imagine a big explosion.

(gunfire and explosion) So we knew everybody in the vehicle was dead.

>>An attack in Yemen this week killed a top Al Qaeda leader... >>The US government called the attack highly successful... >>PRIEST: The CIA had fired an armed Predator at a car driving in the desert in Yemen with a weapon that we didn't know they had in a way that we had never seen anybod do anything like this before.

>>DELONG: It's just war.

It's no different than going to the store to buy some eggs; it's just something you got to do.

These guys, these are the same people that had just killed over 3,000 people in the twin towers and killed over... almost 200 people in the Pentagon.

This was easy.

>>PRIEST: It just begged so many questions.

Is this assassination?

You know, what rules are they operating under?

>>Still, it raises a host of new questions.

>>Does the Director of Central Intelligence now have a James Bond-style license to kill?

>>NARRATOR: Drone attacks were only a part of Greystone.

In Afghanistan, the military captured thousands, but some of the high-value terrorists disappeared.

>>PRIEST: I know from the military people who were on the ground that not everybody was going into the military penal system.

So where were they going, and what were they doing with them?

>>NARRATOR: Only later did Priest learn that Cofer Black and the CIA were using harsh techniques to extract information.

>>PRIEST: Someone uses the term, "Well, these are called 'stress-and-duress' techniques."

And that sort of crystallizes "'stress-and-duress' techniques, that doesn't sound like the military rules."

>>NARRATOR: In secret, the administration had authorized the CIA to use what they called "enhanced interrogation techniques."

>>RIZZO: The enhanced interrogation techniques were a set of techniques that would work on someone who was thought to likely have information about a possible next imminent attack on the homeland.

>>CANNISTRARO: They can do a lot of things that used to be considered torture.

Waterboarding, for example.

By any definition, it's torture.

The Justice Department called it "enhanced interrogation methods" and approved seven of them, including waterboarding.

>>NARRATOR: Al Qaeda's Khalid Sheikh Mohammed was waterboarded 183 times.

It took reporter Dana Priest years to piece together where prisoners like Khalid Sheikh Mohammed were.

They had been hidden in a secret network of CIA prisons known as "black sites."

>>PRIEST: In the investigation of the black sites, I found a worldwide system of about two dozen prisons throughout the world run by the CIA, paid by the CIA, organized by the CIA, but with cooperation from other countries.

>>NARRATOR: Top CIA official John Rizzo helped authorize the prisons.

>>RIZZO: Creating a prison system was something, certainly in my 25 years, we had never done.

It was essential that these people be held in absolute isolation, with... with access to the fewest number of people.

That quickly led to the conclusion that... that facilities had to be built overseas, secret facilities.

>>NARRATOR: For the first time, the White House had approved the building of an international prison system entirely in secret.

>>PRIEST: The amount of secrecy is phenomenal.

The desire and the willingness of government to operate in secret and to deny the public, the media, the basic facts about what they were doing was all-inclusive.

We were falling deeper and deeper into a secretly-run government.

>>NARRATOR: And the secrecy was spreading.

At the Pentagon, by 2002, Donald Rumsfeld was waging his own covert campaign inside the Defense Department.

>>PRIEST: The CIA was very much in front of the military, and that bothered Rumsfeld greatly.

And he would write memos saying, "This cannot stand.

We have to create a capacity ourselves."

>>RUMSFELD: The only defense against terrorism is offense.

You have to simply take the battle to them.

How do you do that?

You don't... you don't do it with conventional capabilities.

You do it with unconventional capabilities.

>>IMMERMAN: Rumsfeld was something of an empire builder, you know-- to create as much power in his department as possible.

>>NARRATOR: Quietly, Rumsfeld expanded the Pentagon's most secret group: Joint Special Operations Command, JSOC.

>>IMMERMAN: It provided a capability within the Pentagon that the Pentagon didn't have before and was not considered appropriate for the Pentagon to have before.

>>NARRATOR: Buried deep inside the Pentagon bureaucracy, Rumsfeld anointed JSOC with power and money.

>>MacGREGOR: One of the reasons that Secretary Rumsfeld became very enamored of special operations forces was the readiness of special operations forces to deplo and do what they were asked to do, whereas the Army presented resistance.

>>NARRATOR: JSOC began a systematic series of capture and targeted killing operations.

One by one, they aimed for Al Qaeda leaders wherever they found them.

(explosions) Using conventional war authorities, they did it all with less oversight than the CIA.

>>CLARKE: So, in the past, covert action was done by CIA, the President had to approve covert action and notify the Congress.

Now, a lot of what looks like the same sort of thing-- covert action-- is done by JSOC.

Now, they say when they do it, it's not covert action; it's a military operation.

So the President does not by law have to approve every operation, and the intelligence committees are not notified.

>>NARRATOR: Then, in Afghanistan, a story circulated that Rumsfeld wanted to use JSOC forces on a new battlefield: Iraq.

>>SCHROEN: You could see changes being made in the US military staffing in Afghanistan, that the Green Beret units-- the 5th Special Forces group, for the most of it-- were being pulled out to refit and get ready for Iraq.

And it was clear that the kind of guys that I think a lot of us believed were essential US military personnel with special operations capabilities were being pulled away.

>>SCHEUER: By 2002, in the springtime, it was almost taken for granted that we were going to go to war with Iraq.

>>NARRATOR: The President needed a convincing reason for war with Saddam Hussein.

George Tenet and the CIA said they had no evidence Saddam had helped Al Qaeda, but Secretary Rumsfeld did.

A secret unit at the Pentagon claimed it had found a connection.

>>GOODMAN: They needed an office that would produce the intelligence that the CIA wouldn't produce.

Rumsfeld said, "I can solve your problem," and they created the Office of Special Plans.

>>BENJAMIN: So they're going to do their own analysis.

They're going to show what the CIA's been missing all along about the true relationship between Saddam and Al Qaeda.

>>NARRATOR: They worked in a vault deep inside the Pentagon.

They had what is known as "all source clearances"-- total access to intelligence information.

>>MALOOF: I went into the system, our classified system, to see what did we know about terrorist groups and their relationships, as well as their connection, associations with not only Al Qaeda but also with state sponsors.

>>NARRATOR: The information was rarely vetted.

Instead, it moved up the chain of command to the office of the Vice President.

>>GOODMAN: And this became material that was then used, sort of in white paper-like fashion, to be leaked to journalists or to create links between Saddam Hussein and Al Qaeda.

>>NARRATOR: It was delivered to the American public and the world... >>CHENEY: New information has come to light, and we spent time looking at that relationship between Iraq on the one hand and the Al Qaeda organization on the other.

And there has been reporting that suggests that there have been a number of contacts over the years.

>>NARRATOR: ...and they began relying on a new phrase, "weapons of mass destruction."

>>RICE: But we don't want the smoking gun to be a mushroom cloud.

>>POWELL: Leaving Saddam Hussein in possession of weapons of mass destruction for a few more months or years is not an option, not in a post-September 11th world.

>>A rapid series of 40 explosions lit up Baghdad in the early morning hours.

>>Military officials have been using the term "shock and awe" to describe the assault on Iraq.

>>NARRATOR: By the spring of 2003, the US had attacked Iraq.

Fast and mobile, Rumsfeld's JSOC teams secretly paved the way.

>>...are now reported to be about 30 miles from the outskirts of... >>NARRATOR: Fighting a conventional war unconventionally seemed at first to work.

>>RUMSFELD: Scenes of free Iraqis celebrating in the streets, riding American tanks, tearing down the statues of Saddam Hussein in the center of Baghdad, are breathtaking.

>>BUSH: On September 11, 2001, our freedom and way of life came under attack by brutal enemies who killed nearly 3,000 innocent Americans.

>>NARRATOR: On the night of 9/11, the CIA had planned a secret war abroad.

>>BUSH: And since September 11, we've been on the offensive against the terrorists plotting within our borders.

>>NARRATOR: At home, another front had been opened: the battle to protect the American homeland.

>>ASHCROFT: We had to move from proving what happened to preventing something from happening because the costs that came with a mass destruction event like 9/11, we can't allow that.

>>NARRATOR: The President asked the nation's largest and most secret intelligence agency to step forward.

>>HAYDEN: A couple weeks into the war, we were asked, "Is there anything more we can do to defend the homeland?"

>>NARRATOR: At that time, Michael Hayden ran the National Security Agency, the NSA.

>>HAYDEN: We began a conversation with the Vice President and then with the President, saying that, "Here are some additional things we could do, "but we cannot do them because we do not currently have the authorities to do them."

That was the basis of the evolution of what became the Terrorist Surveillance Program.

>>NARRATOR: The Terrorist Surveillance Program authorized the NSA to intercept certain telephone calls and emails of American citizens without a warrant.

>>HAYDEN: It clearly was atypical when it came to where the traditional boundaries of the National Security Agency had been, when it came to communications, one end of which was in the United States.

That was a change.

>>PRIEST: Nobody was in a mood to say, "Well, wait a minute.

Are you infringing on privacy?"

You know, privacy versus another 9/11 attack, there was no real question about what was going to win over that.

>>NARRATOR: From inside their secure Maryland headquarters, the NSA was now focused on trying to prevent the next terrorist attack.

>>HAYDEN: I began to lay out to the people of NSA what our mission had become, and it was clear it was going to be counterterrorism.

I said we will be shifting over to the offense and that we would be an integral part of that offensive move.

>>NARRATOR: The NSA created a global electronic dragnet capable of reaching into America's communication networks, capturing 1.7 billion intercepts every day.

>>CLARKE: The National Security Agency has a huge vacuum cleaner around the world, and it is sucking down information from computer networks, from radios, from telephone calls all over the world.

So much information that no human being could ever go through it on a daily basis.

>>PILLAR: The other basic challenge is in sorting through the huge volume of information.

The analogy is not so much a "needle in a haystack," it's "a needle in a stack of needles."

>>NARRATOR: But finding the exact needle would take manpower, lots of it and in a hurry.

The NSA turned to a new force in the covert war: private contractors.

>>PRIEST: You had this boom in the corporate intelligence world, as well.

Companies like CACI, Lockheed Martin, General Dynamics, just all the old-fashioned, industrial, were building ships and submarines type corporations quickly moved into the intelligence and information space.

>>NARRATOR: The NSA spent billions of dollars on more than 480 private companies.

Michael Hayden led the effort in the days right after 9/11.

>>HAYDEN: I did it at NSA, George did it at... at CIA.

We... we all did it.

It was a way to go out there and... and to get these capabilities into the flow infinitely more quickl than you would have been able to do had you gone through the government personnel system.

>>NARRATOR: In office parks near the NSA, thousands of private contractors-- many making much more money than federal employees-- help digest data.

>>PRIEST: This war was not a war that required a lot of tanks, a lot of fighter jets.

It required information.

And information flows in a different way and is... is analyzed by machines.

>>NARRATOR: Exactly how much money the NSA was spending in the years after 9/11 is one of the government's most closely guarded secrets.

The agency's budget, like its work, is a state secret.

>>ARKIN: Well, have you actually looked at this building on a satellite map yet?

>>PRIEST: No.

>>ARKIN: It's gigantic.

I mean, it's... it's... >>NARRATOR: In Vermont, a reporter and former defense analyst, William Arkin, spent years trying to track the post-9/11 growth of America's hidden intelligence world.

>>ARKIN: It's a government organization.

It shows up nowhere.

It's in a pizza parlor.

It looks like it's a cover address.

There's no defense organization there.

I'll have to go look at it, or you'll have to go look at it.

>>PRIEST: Okay.

>>NARRATOR: Working with Dana Priest, the two would do what no one else had done: identify one by one the buildings and companies in what they called "Top Secret America."

>>ARKIN: The Defense Policy Analysis Office.

The Defense Program Support Activity.

The Asymmetric Warfare Group.

Project 7116.

The Special Security Organization.

The CIA and FBI and NSA and all the other agencies.

It took me about a year to complete a decent catalogue of the government entities and corporate entities that work in this world.

>>NARRATOR: They discovered they were the only people in the country collecting such detailed information.

The only way they could verify any of it was to go there in person, hundreds of secret locations hiding in plain sight in office parks.

>>PRIEST: This is a gate to... to the NSA?

>>LANE: There's a government facility back in there.

You'll see it better after we turn down this road.

>>NARRATOR: Inside buildings like these, they launch drone strikes, gather and spread secret information, engage in cyber conflict.

>>LANE: You've got Titan in here.

CSC is in one of these buildings.

General Dynamics.

>>PRIEST: So you really have the big mega-firms, the giants of this whole industry here: Northrup Grumman, Boeing... >>LANE: With a security station here at the front where they... they check out the cars and look underneath.

>>PRIEST: Yeah, that... so maybe you should put the camera down now.

>>LANE: Because you just never know who's watching over here.

>>PRIEST: All right, so can we just go over what you have?

>>WILLIAMSON: Sure.

>>NARRATOR: At the Washington Post, Priest and her team compiled what they found.

>>WILLIAMSON: This is the picture that I went up to that public parking lot, and it was totally legal to be there.

>>WILLIAMSON: For the rest of my life, I will never see the world the same way again, especially around Washington.

Yeah, so, had it not been for the leaves off the trees and at night, you just... you would never see this thing.

>>PRIEST: And yet, it's gigantic.

>>WILLIAMSON: These buildings that... they might only be four stories high, but they go down ten stories.

And there's a whole world down there, like shops and places to eat, that you don't know about that's just for them.

>>NARRATOR: They had uncovered a new, secret world that had grown up in the years after 9/11.

>>PRIEST: We could put the dots on the map.

You had an alternative geography of the United States, a secret geography that is so important, that guides how this country keeps itself safe, and yet it is not revealed to the public even though it may be next to your back door.

>>CLARKE: They didn't put it in one place.

If they had, it would have been the size of the District of Columbia.

What they did instead was scatter it around so it fits into the fabric of metropolitan Washington and on up into Baltimore, and it looks like commercial office space.

A huge new bureaucracy that you can't really see.

>>There was more fierce fighting between U.S. forces and the Shiite militia.

>>NARRATOR: In Iraq, by 2004, the war was going badly.

>>...one of several places where there was violence in Iraq over the weekend.

(explosions) >>The number of American troops killed is now over 1,000.

>>Reports of mortar attacks in Baghdad... >>Several others were wounded when a car bomb exploded today.

>>NARRATOR: Rumsfeld's light force wasn't able to stop the growing insurgency.

>>...by roadside bombs... >>PRIEST: There aren't enough troops, and worse, they're in the middle of an insurgenc that they don't know how to conquer.

>>NARRATOR: And they hadn't found any sign of those weapons of mass destruction.

>>KERR: Early on in the war, it seemed quite clear that they were not going to find major stockpiles of weapons, that we were looking at kind of an empty shell.

>>NARRATOR: David Kay had been given the job of finding the weapons.

>>KAY: From very early on, I said, "Things are not panning out the way you thought they existed here."

And it was specific cases, whether we were talking about the aluminum tubes or we're talking about the nuclear program in general, or the biological program.

>>After eight months of searching Iraq for weapons of mass destruction, David Kay reached a simple conclusion: there aren't any.

>>The political stakes are rising in the overestimation of Iraq's weapons.

The cost... >>NARRATOR: It was an intelligence failure that reverberated throughout Washington.

>>...one of the most damaging intelligence failures in recent US history and says the harm to US credibilit will take years to undo.

>>KAY: I think the intelligence community understood that if the American people and the policy makers really understood the message I was delivering, that there would have to be a major shake-up of the way American intelligence is done, because this was just inexcusable.

>>NARRATOR: George Tenet and the CIA took most of the blame.

>>Outraged lawmakers are demanding to know whether the CIA was pressured to come up with answers the administration wanted to justify going to war.

>>NARRATOR: The bipartisan 9/11 Commission proposed stripping the CIA of its oversight of national intelligence.

>>PRIEST: The 9/11 Commission actually suggested that the country have a Director of Intelligence to make sure that all the different agencies would share their dots, and who could be in charge of the agencies in order to make sure that they weren't overlapping, that they were playing well together, that they were getting efficiencies out of the system.

>>BUSH: Today, I'm asking Congress to create the position of a National Intelligence Director.

The National Intelligence Director... >>LOWENTHAL: Congress starts working on the bill, and they produce a bill in almost no time at all.

And there's very little debate and there's very little consideration.

>>NARRATOR: As the bill made its way through Congress, the existing intelligence agencies pushed back.

The Secretary of Defense led the charge.

>>TOWNSEND: The Secretary of Defense was not anxious to lose power, direct authority over the intelligence assets in the Department of Defense.

He felt very strongly and fought very hard not to lose that authority.

>>MURRAY: The authority of the DNI, which was written into the law as it was drafted, was gradually reduced day after day after da to the point where it became almost meaningless.

>>NARRATOR: John Negroponte was the first nominee for Director of National Intelligence.

>>NEGROPONTE: I got a call from Andrew Card, the Chief of Staff for the President, asking me, "How would you like to be the first Director of National Intelligence?"

I didn't know anything about how Congress envisaged the position or anything else.

So, the first thing I did was to download the law, all 200-plus pages of it, to get some kind of sense of what was envisaged.

>>NARRATOR: To run America's $80 billion intelligence community, Negroponte was given a small staff and a few rooms in the old Executive Office Building.

>>NEGROPONTE: The actual Director's office is nonexistent.

There wasn't even somebody to answer the phones when I first got there.

>>POWELL: I recall one time the Secretary of Defense coming into the office and the Secretary of State walking by, peeking in and just chuckling.

And it was all funny to see them crowded around this small table, kind of the National Security team.

>>HAYDEN: We covered the walls with butcher paper and said, "Well, how about this organizational structure?"

I mean, we really did, and then tried to lay it out.

>>NARRATOR: Negroponte quickly discovered he had little authority to bring order to the sprawling intelligence community.

>>NEGROPONTE: There were some things that were lacking.

The authority to hire and fire.

I believe that it would have been better to have more budgetary authorities than... than, in fact, I actually ended up having.

>>KEANE: If you're going to maintain true authorities over a subordinate organization, you will have to have some control over policy formulation of that organization and also the resources that are applied to it.

And much of that does not exist in that position, so you... you have a sort of an emperor without any clothes.

>>NARRATOR: Negroponte served as Director of National Intelligence for just two years.

In the six years it has existed, there have been five different DNIs.

>>BOND: We gave the DNI a lot of responsibilities and high expectations.

In my view, we did not give that person the authorit over the intelligence community to realize the benefits that were supposed to be derived.

>>NARRATOR: Despite the inability to control other intelligence agencies, the DNI did what other bureaucracies inside Top Secret America do: it grew.

>>PRIEST: It started out 11 people in the Old Executive Office Building.

But that wasn't big enough, so they moved to some of the priciest real estate in the Washington area.

And now they are gigantic-- 500,000 square feet, five Walmarts stacked on top of each other.

And if you ask most people in the intelligence world, they don't know exactly what they do still.

>>It's the inauguration da of the nation's first African American president.

>>NARRATOR: In 2009, the new President would inherit a war in Iraq, a war in Afghanistan and terrorism threats abroad and at home.

>>This will be the largest security challenge here since 9/11.

>>...the tightest security for an inauguration ever.

>>NARRATOR: There had even been a threat to the President-elect.

>>PRIEST: A week before, they'd gotten a reasonable tip that there was a plot on the part of a Somalian immigrant to disrupt the inauguration, and they took that seriously.

>>TOWNSEND: There was enough there that you understood, even if it turned out later not to be real, they had an obligation to take it seriously.

>>PRIEST: The Bush administration national security team briefed the incoming national security team about that threat, and it was mentioned that perhaps they should consider canceling the inauguration.

>>NARRATOR: But all of Top Secret America was on hand to protect the President.

>>PRIEST: What was happening behind the scenes was phenomenal.

It was an unprecedented virtual security cocoon.

>>PERREN: We have the Intelligence Operations Center, Tactical Operations Center, and then we have our bomb technicians, our WMD experts, our evidence response team.

>>NARRATOR: They used eye-in- the-sky satellites and hundreds of closed circuit cameras.

>>PERREN: A lot of camera footage, a lot of live footage being fed into the command post.

So everybody's looking at the crowds in real-time, everyone's looking at hot spots in real-time.

>>NARRATOR: They watched the entrances into the city.

Police and their technology were everywhere.

>>PRIEST: You had license plate scanners all up and down the Eastern seaboard on alert.

You had sharpshooters out.

They used the most exquisite technology.

>>CLARKE: Sensors scattered around the city, picking up the wind, analyzing it every minute to see what's in it.

And all of that information being fed in real-time into the operations center.

>>PERREN: Everybody was watching and working, and it was like a crescendo.

Everybody's anxiety level builds up.

The phone calls, you're getting more and more phone calls.

(cheers and applause) (musical fanfare) >>OBAMA: I, Barack Hussein Obama, do solemnly swear... >>PERREN: You... you can feel the tension in the air.

>>OBAMA: ...to preserve, protect and defend the Constitution of the United States.

>>PERREN: And then you can see the collective sigh of relief when the President was sworn in.

>>ROBERTS: So help you God?

>>OBAMA: So help me God.

>>ROBERTS: Congratulations, Mr. President.

(cheers and applause) ("Hail to the Chief" playing) >>NARRATOR: The reports of the Somali threat turned out not to be true, but as the new President took office there was an open question about the future of Top Secret America.

On the campaign trail, candidate Obama had said it should be dramatically reined in.

>>OBAMA: That means no more illegal wiretapping of American citizens.

>>PRIEST: Barack Obama came in pledging a new era of transparency.

>>OBAMA: My administration will take a top-to-bottom review of the threats we face and our ability to confront them.

Too often, this administration's approach to homeland securit has been to scatter money around and avoid hard choices.

>>NARRATOR: Now, the President would be read into the classified programs, receiving daily briefings on threats to the homeland.

>>TOWNSEND: He begins to get the intelligence brief.

He begins to see the substance behind the inner workings of government.

>>CLARKE: You start getting reports about individuals.

"This known terrorist may be on the move from here to there; "this known terrorist was intercepted talking about a planned attack."

>>TOWNSEND: I think all of that-- including what he had to go through in terms of a security briefing for the inauguration-- influences, then, how he sees the threat and his own responsibility.

>>NARRATOR: It didn't take long for the new President to make clear where he stood.

>>RIZZO: His people were... were signaling to us-- I think partly to try to assure us they weren't going to come in and dismantle the place-- that they were going to be just as tough, if not tougher, than the Bush people.

>>NARRATOR: No one in the Obama administration would talk to Frontline about Top Secret America, but the President had reauthorized almost all of the dark side operations.

Greystone, the hunt for bin Laden and Al Qaeda, continued.

>>RIZZO: Authorities were continued that were originally granted by President Bush beginning shortly after 9/11.

Those were all picked up, reviewed and endorsed by the Obama administration.

>>NARRATOR: At home, the President decided to expand the growth of Top Secret America.

>>PRIEST: They've done nothing to roll it back.

They've done very little to look inside of it, to say what is it that works, what doesn't work, what do we really need and, in this time of economic hardship, what don't we need.

>>NARRATOR: The President understood the political realities.

>>CLARKE: There's going to be a terrorist strike some day, and when there is, if you've reduced the terrorism budget, the other party, whoever the other party is at the time, is going to say that you were responsible for the terrorist strike because you cut back the budget.

And so, it's a very, very risky thing to do.

>>NARRATOR: In his first year in office, the massive Department of Homeland Securit began construction of their new $3.4 billion headquarters.

It will rival the Pentagon as the largest government complex ever built in Washington.

And DHS has continued a nationwide spending spree, sending billions of dollars to state and local police.

>>PRIEST: What DHS wants to do is to turn all of the local and state law enforcement personnel into the tipsters for the FBI, into the front line foot soldiers looking for possible terrorists.

>>NARRATOR: DHS funded high-tech terrorism centers around the country.

>>PRIEST: Every state has at least one.

There's 74 fusion centers in the United States.

>>CLARKE: Contractors went in, put in the large flat-screen TVs, put in the "mission control to the moon" kind of facilities.

>>NARRATOR: Now, state and local police are using surveillance cameras, biometric scanners, high-tech license plate readers.

>>STATE TROOPER: The software with the system, when it sees what it thinks is a license plate, it will read it using OCR, optical character recognition, and make a crosscheck against a database.

>>NARRATOR: While it's been a high-tech bonanza for the states, there are questions about its effectiveness.

>>CLARKE: You can look, if you're objective, at all of this money and all of this effort and say, "What would have happened if we hadn't done that?"

And in almost every case, nothing would have happened.

>>NARRATOR: One troubling example: at Christmas time in 2009, a young Nigerian boarded a plane from Amsterdam to Detroit.

Somehow evading the security net, he was carrying a bomb in his underwear.

>>...tried to blow up more than 250 fellow passengers.

>>What exactly went wrong?

>>KEANE: He actually got to the point of triggering the device, which means at that point, the only thing that's going to stop that is what happened-- a technical failure or maybe a human failure.

>>NARRATOR: There had been early warnings about Umar Farouk Abdulmutallab.

>>MILLER: The kid had gone to Yemen for training.

>>MILLER: His father had gone to the American Embassy to say, "My son is now with Al Qaeda.

I think he's... he may be a terrorist."

>>There are more questions than answers to that.

>>There were no red flags raised.

>>NARRATOR: But no one in Top Secret America had connected the dots.

>>PRIEST: The information on that person was buried in the 5,000 other pieces of information that the Counterterrorism Center gets every day.

>>MILLER: Because the Nigerian guy's name was misspelled by one letter, he did not pop up.

The little bits of data about him did not... were not correlated.

Those dots were not connected.

>>CLARKE: Google does it.

If you mistype something on Google, it says, "Did you mean this?"

Despite spending all the billions of dollars on databases, that simple spell check "Did you mean this?"

kind of software wasn't operating.

>>NARRATOR: And then, five months later, the Times Square bomber.

>>OBAMA: People can be assured that the FBI and their partners in this process have all the tools and experience they need.

>>LOWENTHAL: The Times Square bomber was a horrendously run operation.

A bunch of vendors in Times Square said to the cops, "There's a problem with this car."

>>KEAN: Both those cases, it was not the intelligence agencies, it was private citizens.

On the plane, it was a private citizen who jumped the guy.

Times Square, it was a vendor saying, "Something's wrong there," letting the law enforcement authorities know it.

So we were lucky, and because we have an alert citizenry.

>>NARRATOR: Then, the Boston Marathon.

(explosion) (screaming) >>Oh my god... >>Two explosions near the finish line just a short while ago... >>Looks increasingly like some sort of terrorist attack... >>First mass casualty terror attack on American soil in a dozen years.

>>NARRATOR: In the immediate aftermath, there were again questions about why Top Secret America had not prevented the bombing.

>>Did the FBI miss a chance to stop the bombings?

Was there a missed opportunit when a warning was perhaps given to the FBI... >>And that's going to be heavily scrutinized... >>NARRATOR: The government asked the public for their help.

>>Today, we are enlisting the public's help to identify the two suspects.

They are identified as suspect one and suspect two.

>>NARRATOR: Even though one of the suspects had been on the radar of America's intelligence agencies years before, the high-tech tools of Top Secret America never identified him as a danger.

>>We consider them to be armed and extremely dangerous.

No one should approach them.

>>NARRATOR: Just hours after the FBI plea for help, the suspects went on a violent rampage.

>>A gunfight on the streets of nearby Watertown left one suspect dead, suspect number one.

>>There are police and SWAT vehicles streaming in that direction.

>>Overwhelming presence of law enforcement.

>>NARRATOR: The hardware of Top Secret America rolled out in hot pursuit.

>>Police have told people to stay home... >>Police are going door to door looking for the remaining bombing suspect.

>>Suspect number two has been cornered in the backyard of a home... >>We heard police talking about he's in a boat... >>NARRATOR: Once again, it was only after a tip from an observant citizen that police finally got their man.

>>Apparently, a woman called in to report blood in a backyard leading to a boat.

>>She called authorities; that led them to this scene.

>>Suspect in custody.

Nobody is to come in the perimeter; it's still a hot scene.

>>NARRATOR: In the wake of the Boston bombing, the question remains: has Top Secret America made us any safer?

>>CLARKE: We're never going to bat 1.000 in stopping terrorist attacks, and we're always going to be that hockey goalie that unfortunately lets one puck go by every once in a while.

>>HAYDEN: Even if we're at the top of our game, it does not guarantee that bad things won't happen to America.

>>CLARKE: When something happens, it's very important that we as a society not panic the way we did after 9/11.

And we all panicked, and we all engaged in sort of wretched excess.

More is good.

A hell of a lot more can be bad.

>>KEANE: Sometimes our expectations of being all-knowing is somewhat unrealistic.

At the end of the day, there are people out there who mean harm to us, are thinking about doing harm to us, are motivated to do it, and we don't know what that is.

That's the reality of it.

>> This report continues online with more on this administration's expansion of Top Secret America: things we still don't know, how many secret programs, and how effective are they?

Read an excerpt from the reporter's book, plus more of our exclusive interview with former top CIA lawyer John Rizzo.

>>They were gonna be just as tough... >> And other key officials.

>>Huge new bureaucracy.

>> Follow Frontline on Facebook and Twitter, or join the discussion at pbs.org.

Captioned by Media Access Group at WGBH access.wgbh.org >> For more on this and other Frontline programs, visit our website at pbs.org/frontline.

Frontline's "Top Secret America: 9/11 to the Boston Bombings" is available on iTunes.