The Pentagon was the headquarters for the United States Department of Defense. In military jargon, referring to the Pentagon is referring to headquarters for the US military. The Pentagon was located just outside of Washington D.C.
While UNITY agent Cate Archer was infiltrating a secret Soviet Army base in Siberia, she found memos referring to a Soviet agent using the code name ANATOLI. ANATOLI's assignment was to infiltrate the Pentagon.
The Pentagon on Wikipedia