Khalid Shaikh Mohammed as well as two of his alleged accomplices -- Walid Muhammad Salih Mubarak bin Attash and Mustafa Ahmed Adam al-Hawsawi -- have agreed to plead guilty to conspiracy charges as it pertains to the 2001 attacks ... and instead of a lengthy death penalty trial ... they'll just serve life sentences.

These guys have been held at Guantanamo Bay since 2006 -- first being held at secret CIA prisons -- and there's been years of proceedings to have them face the many charges over the deaths of thousands of Americans.

An official military letter announcing the agreement between prosecutors and these three men read in part, "In exchange for the removal of the death penalty as a possible punishment, these three accused have agreed to plead guilty to all of the charged offenses, including the murder of the 2,976 people listed in the charge sheet."

One of the key issues about this case is the fact the alleged terrorists have been tortured over the years at various CIA facilities -- something that was a sticking point in their pre-trial proceedings, and which could've made their would-be trials somewhat messy.

Now, prosecutors don't even have to go down that road -- these men will just sit in prison for the rest of their lives.

If you're unfamiliar with KSM ... he's the guy who's long been accused as the architect for the airplane hijacking that occurred on that fateful day -- allegedly, he came up with the whole plot in the '90s and pitched it to Osama bin Laden ... and then trained up the terrorists.