The player is often in control of Major Alex Hunter, a pilot from High Altitude Warfare – Experimental (HAWX) squadron but gets to play one or two missions as other pilots, including Captain Dimitri Ivanovich Sokov of Russian Air Force, Lieutenant Colin Munro of the British Royal Navy and Colonel David Crenshaw of HAWX squadron.

To further discourage the player from using guided missiles, some enemy planes constantly dispense an endless supply of flares, making guns the only option.

There are unique missions in which the player is in control of a UAV, a Space Shuttle, a space-based beam cannon, a free-falling man and a pet peregrine falcon.

After stopping an insurgent attack, a volley of cruise missiles is fired at the Prince Faisal Air Force Base where Crenshaw is about to land.

After his rescue, Crenshaw stays on board an aircraft carrier due to an injured arm and commands a remote surveillance operation with agent Drachev of the Russian Voron agency.

In the aftermath of the fall, the Russian Air Force is sent to support Spetsnaz in recovering stolen nuclear warheads from the separatists in Romaniskhov.

Denisov and Sokov provide air support to the best of their abilities, but their commanding officer General Morgunov orders them to blow up the Nevskaya Dam, allegedly to flood the region and prevent the warheads from falling into enemy hands.

While Sokov is piloting a UAV to kill the separatist leaders, Drachev contacts him and has him listen on a phone call between one of the separatists members and General Morgunov, revealing that the events in Russia had been a ruse for the Russian ultranationalists to sabotage Russia's energy industry and seize control of the Russian government.

When the combined forces of the United States and Europe take the war to the Russian lands, H.A.W.X and Sokov fly a mission on Moscow.

He intends to launch nuclear missiles at every major city of the world, allegedly to kill the so-called mysterious people who control everyone and everything including him and Russia.

The game tells the story of Arrow, a mercenary pilot initially in the employment of DDI, a ruthless private military corporation.

The main adversaries in this game are DDI – whose CEO Rainmaker has world domination plans – and a mysterious mercenary ace codenamed Major Zeal.