Servants of the state turn traitor
Tommy Lee Jones character is a rogue CIA officer who decides to steal nuclear weapons from a battleship. This was a common feature of 90s action movies. Men who once swore to protect their nation now turn against it.
In Die Hard 2, William Sadler plays Colonel Stuart who tries to free a drugs baron due to be extradited to the United States, In the line of fire John Malkovich is a disgruntled CIA agent who wants to kill the President. The Rock sees Ed Harris' general steal nerve gas and threatens to use it on his own country unless he is paid a ransom.
All of these men are disillusioned or disappointed with the country they once served. The end of the Cold War meant that Hollywood could move away from the traditional villains like Russians or Arabs.