The five Guantanamo prisoners seek to justify the attack that killed nearly 3,000 people.
The five include self-proclaimed mastermind Khalid Sheik Mohammed. He has acknowledged responsibility in the past.
In an extraordinary six-page filing with the Military Commissions in Guantanamo Bay, Cuba, Mohammed and the others take full responsibility for the attacks and refute the nine accusations against them, point-by-point, reports CBS News correspondent Bob Orr.
The five men are charged with conspiracy. To that they respond, "This is a very laughable accusation. Were you expecting us to inform you about our secret attack plans?"
As for charges al Qaeda targeted civilians, they accuse the United States of "...attacking us in Palestine and Lebanon..." And they ask, "...was it not you that attacked an entire population in Iraq..."
They label themselves tortured prisoners, and chide the United States saying, "You have no values and ethics and no principals."
President Barack Obama suspended their trial in January as his administration evaluates the war crimes trials.
Meanwhile, alleged al Qaeda sleeper agent Ali al-Marri appeared in a U.S. court Tuesdayafter being held for more than five years as an enemy combatant.
Al Qaeda leaders wanted al-Marri, a computer specialist, to wreak havoc on the U.S. banking system and to serve as a liaison for other al Qaeda operatives, according to a court document filed by Jeffrey Rapp, a senior member of the Defense Intelligence Agency.
Since the terrorist attacks of Sept. 11, 2001, the government has held two U.S. citizens - Louisiana native Yaser Hamdi and Jose Padilla of Chicago - and one legal resident, al-Marri, as enemy combatants. Hamdi was released in 2004 after the government said he no longer posed a threat to the United States and no longer had any intelligence value.