It's time for the grand finale. Run down and get into the zodiac boat. We're driving it and it's just like the snowmobile run. You can spray bullets in front of you with autoaim but your main objective is to dodge the obstacles and stay alive. Price will provide most of the cover fire while you move.

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Go through the main camp and stay close to Shepherd. You can't let him get more than about 150 meters away, so keep that in mind. You can fire at the guards if you want. There's no reason not to and it's kinda cool. Regardless, things don't get too tough until we get out into the open.
Other zodiacs will swing out and attack you, along with a few helicopters. Price is right. You can't stay in the open. Stick close to the outcropping on the left. Then swing back a bit to the right. You need to hug those big rocks to avoid the helicopter. You're stuck in the open after this though. Just wait for it to start the run and cut hard to the left to veer away from it. Take the short break to wear away at the men in the other zodiacs. Just fire your pistol into them and make sure that you don't crash into their boats once you take them out.
Keep going past the RPG guards on the bridge and rush forward. Price should warn you about another helicopter run, so veer off to the left again. Then swing right under the bridge to get away. If you're moving fast, you should miss the third helicopter run and enter the rapids.
You can slow down here a little bit if you want. It might not help at all though. Just try to stay in the center and ride it out until things clear up. Engage the next set of boats that comes in to protect Sheperd. Just open fire on them and they should beach themselves. Swing around and drive fast to avoid one last helicopter run.
Shepherd will call for a report and then swing around to his helicopter. His boat will get on board, but we're not done. Hold the boat steady for Price and let him put a few rounds into the helicopter. There's no way to not go over the waterfall though. Ride out the crash and wait for the finale to load.