The player ("Soap" MacTavish) and Price begin the level in hot pursuit of the traitor, Shepherd. They get into a speedboat and chase him down through the cave and down the river with him driving and Price firing away (Note that Shepherd is invulnerable until the end of the mission). Along the way, Shadow Company and OpFor will be taking potshots at both the player and Shepherd respectively. Price will gun them down using his M4A1 and occasionally M203, but the player can also return fire with a Mini-Uzi while piloting the boat. On higher difficulties, the OpFor in this early stage of the level can be a real problem, especially when they use Technicals; taking them out is essential. Shepherd is not difficult to find, as his location is marked on the player's screen. If Shepherd gets too far ahead, the player will fail the mission.
Eventually, Soap and Price will follow Shepherd through a narrow cave, and into a wide open area. Price advises Soap to "Stay clear of open areas!". This area and subsequent areas are difficult on high difficulties. To avoid dying on this part of the mission, the player should keep their distance from the right shore and enemy Zodiacs (eliminate them if necessary). Enemy Little Birds and their miniguns appear and engage the player; they cannot be shot down so they must be avoided, and are extremely deadly on the Veteran difficulty. After avoiding the first Little Bird, enemies on bridges and occasionally the shores, will fire at the player with RPG's. They should be avoided as they do a great deal of damage if they hit the player.
Eventually, Soap and Price make it to rapids. Though rough at first, the river becomes more smooth as they progress. Hostiles will still attack the player from Zodiacs, on the shores and bridges with RPG's, and Little Birds. As they go along the river, they hear Shepherd and a Shadow Company U.A.V. Operator talking to each other on the radio. The player will then go under a bridge, and see Shepherd's Zodiac race towards a Pave Low helicopter. Shepherd is forced to cut his speed drastically to board the chopper, giving the player a few seconds to catch up. The helicopter starts to lift off just a few feet above your head. When it appears that Shepherd will get away, the helicopter slows down and turns sharply to avoid flying straight into a sandstorm and hovers over a waterfall. With only a few seconds left before the chopper is out of range, Price tells Soap to steady the boat and fires three shots at the helicopter. The first two shots miss, but the third round hits one of the Pave Low's engines, this causes the helicopter to catch on fire and violently snap to the right. As the helicopter starts to spin out of control towards the riverbank below, Price tells Soap to back up, but the current is too strong and they go over the waterfall, plunging into the river moments before the burning Pave Low crashes.
After a brief wait period, Soap wakes up, washed up on the shore. He picks up his knife, and walks towards some flames in the distance. Moments later, he comes upon a Shadow Company soldier crawling away from the crashed helicopter a short distance away. Soap has the ability to knife the soldier, or let him crawl away and bleed to death. At the crash site, he sees another soldier in a position similar to the Last Stand position. The soldier will attempt to fire his pistol, but to his misfortune, is out of ammo. Soap can also knife this soldier or let him bleed to death.
After deciding the soldier's fate, Soap will see Shepherd stumble out of the flaming wreckage of the Pave Low. He will glance at Soap and then run away into the sandstorm. (he cannot be killed) Soap follows him and finds him leaning on a car.
If Soap waits a moment, Shepherd will tell him to go ahead and kill him, although it won't change anything. If Soap waits another moment, he says that he "Knew you [Soap] couldn't do it". He then says Soap is a good warrior but that he couldn't take that extra step to do what was absolutely necessary.
Once Soap attempts to knife him, Shepherd will block his attack, ramming Soap's head into the car, causing Soap to fall. Shepherd pulls out his own knife and jabs it deep into Soap's chest causing Soap to black out from the trauma.
While Soap is coming to, he hears Shepherd speaking: "Five years ago... I lost 30,000 men in the blink of an eye, and the world just fuckin' watched.". His vision returns to see Shepherd standing over him, loading two rounds in his .44 Magnum Revolver, while saying, "Tomorrow, there will be no shortage of volunteers, no shortage of patriots," He cocks the hammer of the pistol, ending: "I know you understand,".
Just then, Captain Price intervenes, tackling Shepherd and kicking the revolver out of his hand before Soap is executed. Soap then crawls towards the pistol, (the player needs to do this manually by using the left and right triggers/mouse buttons) in hopes of using it to kill Shepherd. Before Soap manages to grab the Magnum, Shepherd knocks Price down and kicks away the pistol, which was almost within his reach. He stomps on Soap's face, and he blacks out.
Soap wakes up a few seconds later to see Price and Shepherd engaged in brutal hand-to-hand combat. After a few brief moments, the fight begins to turn in Shepherd's favor as he knocks Price down to the ground. While, Shepherd is slowly and relentlessly beating Cpt. Price, Soap notices the knife still stuck in his own chest. He painfully pulls it out (accomplished by the player repeatedly tapping the "use" button) and spins it around in his hand. He looks over at Shepherd (who has just about beat Cpt. Price to death), and just as the General looks up, the severely wounded Captain MacTavish throws the knife at Shepherd's face, which lands in his left eye, killing him.
Soap almost blacks out before Price wakes up and stumbles towards him. While Price attends to Soap's wounds, he notices a Little Bird helicopter land on the riverbank behind them. Price tells Soap the bandages will hold for now and helps Soap to his feet. Nikolai, the pilot of the Little Bird, comes to assist Price and Soap. He mentions that because of what they have done, that they'll be looking for them now. Price tells Nikolai that they need to get Soap of out there, and Nikolai says he knows a place to go, and the game ends as Price and Nikolai are carrying Soap to the helicopter.
Intel No. 45: Right before you get on to the boat, look left, it's on the crate (with lights shining on it). This Enemy Intel is considered to be the easiest to find throughout the game, yet it may be surprisingly easy to miss due to the hectic pace and Price urging you to get on the boat.