According to the Washington Post, January 20, 2002, "The Last Watch," the entire chain of command of the super secret Chief of Naval Operations Intelligence Plot (CNO-IP) were killed in the September 11 attack on the Pentagon. The first floor of the western wedge of the Pentagon was occupied in part by the office of the "Chief of Naval Operations Intelligence Plot", who had moved into their new offices (earlier than most other occupants). 42 out of 50 Naval personnel working in the newly relocated Naval Command Center were killed.

http://www.washingtonpost.com/ac2/wp-dyn?pagename=article&node=&contentI...

[...]Only those with the highest security clearances, above top secret, are privy to their work. Even in the acronym-happy Pentagon, the term CNO-IP is obscure.

It stands for Chief of Naval Operations Intelligence Plot. Its small, typically young staff keeps a round-the-clock watch on geopolitical developments and military movements that could threaten American forces. "We keep an eye on the bad guys," those assigned to the unit would tell outsiders, batting away further questions.

[...]

It could have been any one of the scores of memorial services held after the Sept. 11 attack on the Pentagon, but no reporters were supposed to know about this one. Only later was a videotape of the ceremony stamped "unclassified." It revealed just a sliver of the story of the CNO-IP, which had lost its entire chain of command.

[...]

When hijacked American Airlines Flight 77 hit the Pentagon at more than 500 mph, slamming through concrete and corridors, spewing fuel and fire, it destroyed much of the Navy Command Center. It smashed directly into the offices of the CNO-IP.

[...]

In mid-August, people boxed up their office files and family photos. Finally. The CNO-IP was moving to renovated offices in the Navy Command Center, on the first floor of the D-Ring, on the Pentagon's west side.

This Naval Intelligence office was responsible for breaking open the Jonathon Pollard affair. Naval Intelligence was the base from which Jonathan Pollard operated. It was Naval Intelligence that caught Pollard and Naval Intelligence that insisted the FBI arrest him.