The story begins in the middle, with Nate and an individual named Sam being pursued in a boat. Hold R2 to accelerate the boat toward the island and don't be afraid to smash into the smaller boats to destroy them.
When the larger boat rams into you and begins to drop mines you'll want to avoid them as much as possible, but you'll eventually get hit and Nate will be flung from the boat. Hold X to surface and when you spot the incoming boat headed your way hold O to submerge and narrowly miss the propeller.
When you resurface and swim to the boat Sam will take over fixing the engine while you provide cover. Take cover on the same side of the boat that Sam is on and prepare for a firefight.
The first boat has two normal enemies at first, but when you see an armored enemy rush to the left side of the boat you'll want to focus on him. This enemy uses a Grenade Launcher and can do heavy damage, but if you defeat him quickly he'll blow up his own boat.
Two smaller boats will speed up alongside you, each with one enemy, and when you defeat the closest boat another boat with two more enemies will take its place.
Once the smaller boats are gone and Sam has repaired the engine, take the wheel and head toward the island again. This time you're going to want to avoid the rocks as you weave through the area and ram into the smaller boats.
After a while the large boat will reappear and ram into your boat, capsizing it and flinging Nate into the water.