The story begins in war-wracked Somalia, where the most powerful warlord in the country, Akil Farrah, has managed to overthrow the ruling government and proclaims himself President.

His superior, General Cleveland, informs him that he and the JTF First Battalion will be sent to Somalia to remove Farrah's regime, and grants him the jurisdiction to do whatever it takes to succeed.

In the first mission in the game, O'Connell successfully secures a cargo ship suspected to be used as an arms transport at Port Mogadishu.

Cleveland informs O'Connell that the reporter in question is Pepper Morgan, a world-renowned war-correspondent who has connections to all of the major TV Networks.

Back at base, where the JTF troops are celebrating, O'Connell sits alone in a dark locker room, where he remembers having fought in a battle in Somalia in the 1990s with another man.

Running low on ammo, O'Connell is ordered by the unknown man to booby-trap a prisoner with a grenade, before both of them flee.

At some point after the first mission in Bosnia, Dragović's fighter-bombers rupture the Kraduvice Dam, flooding many villages and forests.

After the riot, O'Connell's men are told to capture the original clan leader's brother, who is later found to have died from lead poisoning.

After questioning a captured Russian pilot, the JTF investigates a rebel's cave complex, which leads to an old Soviet ICBM missile silo, where the JTF finds an ex-CIA agent, named Courtland, who has a reputation for interrogating and then executing prisoners, for acting as a lone wolf, and is revealed to have been the mysterious man from O'Connell's flashback.

Heavily armoured vehicles such as the M1A2 Abrams tank and the M2A3 IFV are airdropped in by a Hercules transport plane onto a captured runway.