FBI/CIA/Fed prosecutors too busy trying to bring W down and build Clintoon's breastacy.
That is a motive, but I think a secondary motive. These folks, Guiliani foremost when he was a prosecutor, are motivated by self-interest first. They don't care for right-wrong, justice-injustice, or anything else. They care about their political careers and making a name for themselves.
When he briefly left the noisy room with this call, someone in the FBI grabbed the briefcase, and sure enough, he had taken homework with him, a few classified documents. Enough to "have something on him."
He made waves.
Mr. O'Neil thereafter, took the job as security chief of the World Trade Center, where he died, 9-11-2001.