In modern popular culture, there are numerous depictions of different government agencies in conflict. The reasons for this range from competition over funding, conflicting goals, ect.
A few examples (some spoilers if you watch/play these):
In the X Files where there is conflict over whether or not the existence of Aliens should be public knowledge
In the Grand Theft Auto video games series, two fictional government organizations called The Agency (likely the CIA) and the FIB (likely the FBI) are constantly in conflict over funding, taking credit for cases, and controlling witnesses
In the show Sons of Anarchy, the Federal case against a motorcycle gang is not brought up because leaders of a drug cartel they're selling weapons too work for the CIA.
My questions are the following:
While these are all fiction, is there any basis in fact?
What are other moments in the post-WWII era in which U.S. governmental agencies were in conflict with each other.
While less flashy the inter-service conflicts between the branches of the armed services have been with us since the founding of the nation.
Though perhaps got no more heated than in 1949 with the "Revolt of the Admirals". Essentially when an anti Navy and Marine Corps SECDEF took charge the tensions between the Navy and the Air Force over unification as the DoD and the future structure of the military boiled over.
The cancellation of the first large postwar carrier, the USS AMERICA, caused outrage in the fleet and led the SECNAV to resign. In very public hearings before Congress the Admirals questioned the ability of the Air Force to effectively protect the nation through nukes alone, while the Truman Administration saw this as disloyalty.
While Congressional hearings found no outright wrongdoing they rebuked Secretary Johnson fro not including Congress in the decision to can the ship and for his ham fisted handling of balancing the services budgets.
The Navy would in large part be vindicated less than a year later when the Korean War broke out. Due to the budget cuts Army and marine formations were woefully under prepared for combat, and the Navy was so short of ships that they couldn't even enforce a blockade of the limited coastline of Korea.