The story ends in an unknown location. A scientist is shown, making a formula for an unknown reason. Suddenly, an unknown group of men in black suits appear, destroy everything in the facility, and kill everyone in it. The scientist--being able to hide this long--managed to escape, but was soon caught by the men in black. The men notice the scientist, and take immediate action. But then, a soldier in a military uniform appears from an airvent above where the scientist and the unknown men were... "fighting". The soldier kills the men in black, and saves the scientist. The scientist--startled--asks for the soldier to get him out of there. The soldier agrees, but at a cost that the scientist must answer his questions...
A flashback occurs. You and your team attempt to suppress a rebellion located in South East Asia. Bull, one of your allies, was hit while fighting. But it was not a major wound, and Bull survives. After succeeding to suppress the rebels and terrorists, the Strike Force Squadron heads back to base. But are then ambushed by unknown enemy MiG's, and out from those jets came out unknown men in black. Jenkins--the pilot of the plane--is willing to aid you. The Strike Force, along with Jenkins, succeeds in killing them, but the battle caused too much damage, and they were forced to jump out of their plane.
They land on an unknown remote island, and are scattered all over. The player lands on a section of the island filled with soldiers who seem to be bloody and disarrayed. The player and Jenkins attempted to help the soldiers, only to find out they don't want help. The bloodied soldiers shoot Jenkins and the player. Unfortunately, Jenkins fell victim to the same toxin the soldiers had apparently inhaled, and became as disarrayed as them. The player was forced to kill Jenkins, and his once allies.
After successfully killing Jenkins and the "infected" soldiers, the player meets with Shadow--a member of his squad: pilot, CQC expert and sharpshooter--and they hear a large explosion. They attempt to see what happened. Both Shadow and the player enter the facility, and in there, they find slaughtered soldiers and scientists, and the same unknown enemies that destroyed their plane. They successfully kill the men, and they save a scientist. The scientist asks for help, and wishes to get out of the facility. The player answers, agreeing, but only if the scientist would agree to answer his questions...
The player starts by asking the scientist what had happened to those soldiers--as well as Jenkins. The scientist replies that they were developing a new kind of nerve toxin, to be used against infantry soldiers. All infected would lose the will to fight. But something went wrong with the toxin, and instead of making soldiers lose morale, it shut down all brain activity except for the Reptilian Region--The same region that gives you adrenalin. The scientist says that there is a cure, but they will need to find certain plants. And so, the Strike Force--now regrouped--look for those plants. But the unknown men in black ambush them. They fight for their lives, and the plants. Fortunately, the unknown men failed, and the plants were given to the scientist. The scientist then completes the formula, and successfully creates the cure. They attempt to find a way to somehow spread the cure, and save all those infected.
While the scientist finds a way to spread the cure, the Strike Force attempts to ambush their enemies, and retrieve their intel. They succeed, and Toad--The team's medic and scout--finds out they are an organization called "Globex". He also finds a file, showing a mysterious man, informing his men to ambush the facility once again, and kill all survivors.
With that, the Strike Force attempts to protect the facility--as well as the scientist. They failed, and the facility was destroyed. The facility was now overrun with the Infected. But they manage to save the scientist, and all of the remaining data the scientist created.
The Strike Force attempts to capture more data from Globex, and they ambush another HQ. They succeed in finding the data, but find out that Globex plans to launch a nuke to kill everyone infected, as well as everyone in the country--to avoid infection. The Strike Force boards the train carrying the Globex nuke, and they attempt to stop it. They fail, sadly, and the nuke was launched. As a last ditch attempt, the player and Shadow--both in a helicopter--attempt to go up towards the nuke, and try to replace its warhead with the cure. Unfortunately, Globex finds out about it, and they send in MiG's and infantry to stop the two of you. The player attempts to protect the chopper while Shadow drives it. He succeeds, and Shadow drops off the player in the Nuke.
Afterwards, the player tries to replace it's warhead, with the cure, while defending himself from Globex infantry, and listening to Shadow, who he expects to give him the instructions about the nuke. He succeeds, and just when he thought the battle was won, Globex sends in their leader, and he fights the player, one-on-one.
It seems as though they are evenly matched, but eventually the player manages to weaken the Globex Leader seriously. But the Globex Leader would not give up, and he attempts to die along with the player. But the player would not allow that, and he replies to the Globex Leader with one sentence:
"Sorry, but I fly solo."
He releases his parachute, and watches as the Globex Leader angers, but soon unseen, due to the Nuke's explosion. The player has done it. He has defeated Globex, its leader, disarmed their nuke, and saved millions of lives.
As the battle against the Infected rages on the ground, the cure spread over in the air. Those who have been cured were unaware of how close they came to annihilation, and they thank the Strike Force. "The world would have been engulfed in flames, were it not for that scientist..." The player said, "... Actually, I never caught his name..."
Several weeks later, the final cutscene shows the Scientist contacting someone, who sounds just like the Globex Leader. The Scientist informs him of the toxin, and apologizes for it's spreading. The man replies, asking if the scientist had "dealt" with the "soldier" and the scientist replies saying "No, but he has no idea of our true intentions. We were able to save some of the toxins and the cure." The man congratulates the scientist, and the conversation ends with one final reply from the scientist: