I just watched the pilot episode for the short-lived X-Files spin-off, The Lone Gunmen. And in an eerie coincidence, the March 2001 episode offered a conspiracy theory for the World Trade Center attacks six months before they actually happened.
The scene opens when Byers (the geek with the beard) discovers that his father faked his own death because he'd uncovered a government plot.

BYERS' FATHER: John.
BYERS: Dad!
[His father slaps him]
FATHER: What the hell are you doing? Why didn't you stay out of this? Leave me buried!
BYERS: What is scenario 12-D?

BYERS: We know it's a war game scenario - that it has to do with airline counter-terrorism. Why is it important enough to kill for?
FATHER: Because it's no longer a game.
BYERS: If some terrorist group wants to act out this scenario, why target you for assassination?
FATHER: It depends on who your terrorists are.
BYERS: The men who conceived of it in the first place! You're saying our goverment plans to commit a terrorist act against a domestic airline...
FATHER: There you go, indicting the entire government as usual. It's a faction. A small faction.
BYERS: For what possible gain?
FATHER: The cold war's over, John. But with no clear enemy to stockpile against, the arms market's flat. But bring down a fully-loaded 727 into the middle of New York City and you'll find a dozen tin-pot dictators all over the world just clamoring to take responsibility and begging to be smart bombed.
BYERS: I can't believe it. This is about increasing arms sales! When?
FATHER: Tonight.
BYERS: How are you going to stop them? Why don't you tell the world this? Go to the press!
FATHER: You think I'd still be drawing breath 30 minutes after I made that call. The press? Who's gonna run this story?
BYERS: We would.

FATHER: This? It's a bird cage liner. Wild-eyed crap, right up there with "Elvis is an alien" and two-headed babies.
BYERS: You obviously read it.
FATHER: Don't be so damn naive. You think this is gonna save the world? I'm doing what I can, John. I don't have all the specifics on Scenario 12-D, but I think I know the flight they've chosen. You stay out of it. I don't want them gunning for you too.

Byers and his father board the flight - which leaves for Boston - while on the ground the geeks (Frohicky and Langley) tap into the plane's on-board navigation system.

FROHICKY: I'm in. We've got ourselves a convoy.
BYERS: What's your progress?
LANGLEY: I hacked into the flight control system output.
FROHICKY: With a little bit of help!
LANGLEY: It's what the brains of the plane is telling the little black box.
FROHICKY: Course, heading, attitude, hold, yaw, access stabilization, w-- what the heck's that?
LANGLEY: Is that what it looks like?
FROHICKY: I think it is what it looks like.
BYERS: What does what look like?
LANGLEY: Modem protocol. Remote access. Somebody on the ground's flying your plane.
          [On the ground]
BAD GUY #1: Bogie, sir.
BAD GUY #2: Keep your course.
BYERS: I need to know our flight plan.
FROHICKY: I'm mapping the data now.
LANGLEY: Byers, your flight's going to make an an unscheduled stop. In exactly 22 minutes.
FROHICKY: Corner of Liberty and Washington. Lower Manhattan.
BYERS: World Trade Center. We're going to crash the plane into the World Trade Center.
BYERS' FATHER: I'll tell the flight crew.

On the ground, the geeks scramble unsuccessfully to unlock the plane's navigation system. On the plane...

FATHER: Your friends have failed, haven't they.
BYERS: There's still hope.
FATHER: I hope my next funeral's as nice as my last one.
          [Footage of plane flying towards World Trade Center]

The geeks' computer screen suddenly displays the words "Manual override unlocked."

LANGLEY: B-i-n-g-o! We've got manual override!

          [The plane veers up.
          It flies over the World Trade Center.]

Byers and his father leave the plane, as Byers talks about exposing the plot to the FBI.

FATHER: God I see myself in you. The same youthful enthusiasm, idealism... I was so angry at you, for so long, because I didn't want you to waste your life tilting at windmills. But I see now that you've got something that I never had. You're a brave man, John.
BYERS: You're not going to testify. You're going to let them cover this up.
FATHER: They almost killed me twice They won't fail a third time. My silence will keep me alive. And you.
FATHER: I know you and your friends are fighting for the American dream. Just don't expect to win.