This is a partial transcript from The War on Terror: The Hunt for the Killers. For a complete transcript of the entire broadcast click here.

LAURIE DHUE, HOST:

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ROBERT MUELLER, FBI DIRECTOR:  I think we are worried about al Qaeda operatives leaving through Iran.

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DHUE:  FBI Director Robert Mueller in Pakistan today, questioning Iran's commitment in the coalition against terror.

Well, joining me now is a former CIA operative who says bin Laden met with an Iranian intelligence official in 1996 to establish ties.  Robert Baer spent ever 20 years in the CIA, mostly in the Middle East, and has written a new tell-all book which sharply criticizes his former agency for its intelligence-gathering.  The book is called See No Evil: The True Story of a Ground Soldier in the CIA's Counterterrorism Wars.

Welcome, Mr. Baer.

ROBERT BAER, SEE NO EVIL, AUTHOR:  Thank you for having me.

DHUE:  I'd like to point out that in 1998, the CIA awarded you their career intelligence medal.  All right, we'll get to your book in just a moment.  But first, today we saw the first hearing into the Enron debacle, and yet it has been four and a half months since the September 11th attacks, and so far not one hearing and what went wrong.  Does that surprise you?  And why hasn't there been one?

BAER:  On Enron?

DHUE:  No, I'm saying we've already had a hearing on Enron, and yet it's been five months since the September 11th attacks and there has not been a hearing on what went wrong in the intelligence community.

BAER:  Oh, absolutely.  I mean, we should -- we should look into this.  We don't need to assign fault, but we should look into it.  Something went wrong.  It was a failure.  We have to get to the bottom of it.

DHUE:  Your book goes into detail about exactly what might have gone wrong in the fight against terrorism.  You say September 11 was the result of a series of mistakes.  What are the biggest mistakes?

BAER:  They were systematic through the entire government, from the State Department issuing visas to those 15 Saudis without interviews, was a mistake.  Immigrations failed.  Not keeping track of these people.  The FBI failed, not having sources, and the CIA failed.  We all failed, as a people, as did the press.  And it's time to turn the corner on this.

DHUE:  What has to happen for the corner to be turned?  Do you think that the CIA is going to have to become less hamstrung by the U.S. government?

BAER:  The CIA was politicized from the '60s on, and it got worse and worse every year.  We can turn this around, and I'm sure it's being done right now, but it's going to take years.  It's going to take four or five years.

DHUE:  One of the things you talk about in your book is in 1996, bin Laden establishing this kind of alliance with Iran.  Iran is saying now that it has not and it will not harbor any terrorists.  But historically, you point out that Iran has had more terrorist activity than Iraq.  So how do we trust these guys?

BAER:  We can't.  The minister of defense was directly responsible for holding the hostages in Lebanon in the 1980s.  How can we ever trust this man?  He is the person sending arms in to western Afghanistan now, into Herat.

DHUE:  How close would you say the relationship or the connection is between Usama bin Laden and Iran right now?

BAER:  There is a direct connection.  In 1988, Iran set up relations with the Egyptian Jihad and continued all along.  And we've had many indications, which have appear in the press, that Iran set up relations with bin Laden in 1996, or even earlier, 1995.

DHUE:  Well, that's a long time ago, and it's very disappointing when you consider what has happened in the last four months.  And talking about finding bin Laden, the trail has gone cold, if it's not completely dead.  What does that say about our intelligence capabilities?  Is the ball being dropped yet again?

BAER:  We have a long way to go.  The fact that bin Laden and his extended family have apparently escaped worries me.

DHUE:  How much does it worry you?  And do you think we're ever going to get him?

BAER:  Oh, we'll get him one day.  But the fact that we had no sources in his entourage or anywhere close, to know where he is, is another failure.  We have to overcome this.

DHUE:  Do you think Usama bin Laden is dead, or do you think he's perhaps regrouping, planning another attack a year from now, three months from now, whenever?

BAER:  I think he's alive and he's planning another attack.

DHUE:  Very, very scary.

BAER:  At his timing.

DHUE:  Oh, boy!  You know, CIA officials have an obligation to not talk about secret information, but you have exposed a lot in this book.  How were you able to do that?

BAER:  I submitted the text to the CIA, and it was cleared and corrected by the CIA where I'd made mistakes.  I was very pleased with the process.

DHUE:  So it was thoroughly vetted as you went along?

BAER:  Absolutely.

DHUE:  OK.  And what kind of a -- what kind of a response did you get as you were going through that process?  Were people angry that you were exposing this, or were some secretly patting you on the back, saying "Thank you"?

BAER:  The rank and file was happy, management was unhappy.

DHUE:  And that's all you'll say about it?

BAER:  Yes.

DHUE:  OK.  And I understand that we're going to see this on the big screen at some point, perhaps?

BAER:  Apparently.  Soderbergh and Clooney.

DHUE:  Steven Soderbergh, George Clooney -- not bad at all.  Robert Baer, very quickly, do you think we're going to win this war against terrorism around the world?

BAER:  We'll win.  It's going to take longer than we expect, though.

DHUE:  All right, Robert Baer, former CIA operative, author of the new book "See No Evil."  Thanks for taking the time to talk with us tonight.

BAER:  Thank you for having me.

Be sure to watch The War on Terror: The Hunt for the Killers every weeknight live at 10 p.m. ET on the Fox News Channel for all the very latest news on America at War.