| Summary
| - Immediately after the explosion, six Tu-160 Blackjacks are detected heading for Moscow. The Warwolf is sent to destroy them before the can reach the city. The first five turn out to be a ruse, while the sixth, escorted by Markov himself, sneaks a Trinity into firing range. Bishop destroys the last bomber and engages Markov in a fierce duel over Moscow, finally shooting down his plane. Unbeknownst to him, however, Markov manages to eject.
- The Warwolf Squadron escorts the Russian Sova transport flight to a Loyalist airbase. Upon arrival, they find it under ground and air attack and have leave Sova behind to defend it. After repelling the first enemy wave, the Warwolf lands for refueling but has to take off in a hurry when the second wave arrives, along with Sova. They protect the landing transport planes and proceed to wipe out the remaining enemies.
- The Loyalist Russian ground force prepare to take Moscow back from the NRF and request American close-air support. The Shooter Squadron clears the way for advancing Loyalists but are impeded by NRF's radar grid that prevents them from flying above building height. Doug Robinson's Apache goes on a solo mission to take out the radars. Just as they celebrate victory, the NRF bombs Moscow with one of three remaining Trinities. Robinson is knocked down but survives.
- Nomad and Shooter squadrons attack a rebel hideout in the very first operation of the war. Nomad 62 is shot down, and the gunners of Nomad 61 and 63 provide cover for emergency extraction. During the battle, a Trinity weapon detonates nearby, inflicting burns upon everyone in Nomad and Shooter squadrons.
- Stagleishov attempts to surrender, using the last Trinity to bargain, but Markov kills him and takes control of the coup's remaining forces. The coup's planes attack Miami, reenacting Bishop's nightmare from mission 01. However, Bishop doesn't die, as Guts shields him with his plane in the last moment. Bishop then manages to gun off his jammed canopy so he can bail out into the sea, and gives chase to Markov's PAK-FA carrying the last Trinity.
- Task Force 108 is transferred to Dubai, where they believe Stagleishov and his fellow renegades will strike next. The Warwolf defends the city from multiple enemy bombing runs but none of the attacking bombers carry the Trinity.
- The Prime Minister of Russia, captured by the NRF forces, is found on a yacht in the Black Sea. The Warwolf Squadron and the Loyalist air force attack the escort fleet while Spetznaz secures the yacht and frees the Prime Minister.
- Bishop chases Markov through a massive hurricane off the coast of Florida. Markov is soon joined by his former wingman and secret supporter Major Illich, who also flies a PAK-FA and holds Bishop off at the cost of his life while Markov heads for Washington with the Trinity.
- Shooter and Nomad Squadrons attack and secure three rebel cargoships, which they believe to be carrying the Trinity, but it proves to be a false lead.
- Shooter and Nomad Squadrons, all healed up from their first operation, storm the rebel hideout where Major Illich is being held and break him out. Afterwards, they destroy a convoy of SRN trucks, which turn out to be carrying a Trinity bomb, causing a massive explosion.
- Returning from their last mission, the Warwolf Squadron almost collides with the Russian Big Bear Squadron taking off from the Allied Base in a hurry. The Warwolf follows them but the Russians open fire. Pierre La Pointe reveals them as traitors and orders them shot down. Afterwards, Colonel Markov engages the Warwolf, targeting Guts. Bishop attacks him but is quickly defeated, spared only by Ivan Stagleishov calling Markov off. Just as Bishop barely manages to land, a Trinity explosion levels the nearby town of Carruth.
- Having traced origin of Trinity to ancient caves in Mogadiyu, the Shooter and Nomad Squadron deploy there and plant explosive at the facility, supported by Janice Rehl's Spooky 01 gunship. Nomad 61 commander goes back for one of his men but finds him dead and misses the chopper. Despite taking heavy fire, Rehl successfully executes a of him with her AC-130U.
- Surviving coup forces launch a massive air attack on Washington D.C., with their crippled planes using tactics to destroy the low-altitude air defenses, various F-16 fighter planes including Viper 7, and the USS Anzio and clear the way for Markov and a group of 6 Tupolev Tu-160 Blackjack's. When he finally arrives, Bishop gives chase. The cruise missile housing the final Trinity warhead is damaged, so Markov has to fly close to the White House before firing it. Just as he is about to succeed, he is killed by Bishop, who then races after the missile, barely shooting it off course.
In the epilogue, Bishop is greeted back at base by Janice Rehl and a cheering crowd. His inner monologue reveals pride at having mastered his nightmares. A short scene after the credits shows Guts being located in the sea by a rescue helicopter.
- The Task Force 108 and their Russian allies defend their NATO base in East Africa and the nearby oil facility from SRN troops. While pursuing the retreating fighters, Russian Major Sergei Illich is shot down and captured by the rebels.
- William Bishop dreams of a fierce dogfight over Miami, which ends in him being shot down and killed by Andrei Markov, just as he wakes up.
- A Razor Squadron bomber is sent to destroy the Russian ICBM silos taken over by NRF. Passing undetected through a canyon filled with radars, Rehl's plane bombs the silos, while the Warwolf and Red Moon Squadrons catch up and protect them from enemy interceptors. Major Illich has an engine malfunction and flies off in an unknown direction. Just as they prepare to leave, the last undetected ICBM launches, and Bishop races to destroy it at close range.
- The attacks in Dubai and Suez were just a ruse for the Russian conspiracy Blatnoi's coup d'etat in Russia. Having bought over many top Russian military personnel , they take control of the country overnight. The Warwolf provides to the Loyalist Russian marines of Tyuleni unit's counterattack in Derbent. As they capture the fortress, Markov appears and fires a Trinity missile, but Bishop destroys it in the air.
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| Location
| - United Arab Emirates
- Moscow, Russia
- Washington D.C.
- Black Sea
- Eastern Africa
- Miami, Florida
- Florida Coast
- Dubai,
- Belyi Base, Russia
- Caucasus Region, Russia
- Derbent, Russia
- Hamada,
- Mogadiyu,
- Suez Canal, Egypt
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