The Pentagon was the headquarters of the Department of Defense.
A source in the Pentagon informed Mike Novick about the involvement of Jack Bauer in Operation Nightfall, establishing a connection between Bauer and Senator David Palmer. Later, Alan Optican (a DOD official and associate of Palmer), intervened on behalf of Senator Palmer from the Pentagon and instructed Ryan Chappelle to stop stalling Palmer and give him any access he needed.
Palmer was later given a secret file on Victor Drazen from his source in the Pentagon (possibly Optican), and in it was the address 21911 Kipling in Saugus, which confirmed a lead that Jack Bauer was investigating.
When President Charles Logan was informed of the launch of a stolen American "S-series" Legacy nuclear warhead from Iowa, his adviser, former President David Palmer, recommended that the Pentagon (and Congress) be moved to a secret safety facility.