The story starts in medias res where Nathan Drake and his brother Samuel Drake are being chased through the seas during a storm by Shoreline mercenaries. They race towards an island that is of some importance to the brothers and the mercenaries. Even if they are going as fast as they can, Nate and Sam are being gained upon by the mercenaries in fast speedboats. Sam tries to hold them off by shooting at them but fails to do any significant damage. Realizing that they have the bigger boat, Sam advises Nate to ram the smaller speedboats of the mercenaries.
As they all speed towards the island, a bigger Shoreline ship rams Nate and Sam's boat, damaging it and they drop depth charges in an attempt to kill Nate and Sam. The boat hits one of the depth charges and blows Nathan off the boat. Nathan resurfaces but dives back when a Shoreline boat passes by, narrowly missing the boat's turbines. Nate resurfaces and Sam spots him, who urges Nate to swim faster. The explosion has the damaged the engine and they are stuck in the water. While Sam fixes the engine, Nate holds off the mercenaries. The bigger Shoreline ship stops by and Nate causes a chain reaction that destroys the ship's helm, causing it to speed away.
Sam fixes the engine and they speed towards the island while still being chased by Shoreline. They get close to the island and avoid the dangerous rocks that decorate the island's coast. Before they could get close enough, the bigger Shoreline ship that Nate destroyed appears out of nowhere and rams Nate and Sam's boat, shipwrecking and separating the two. Nate passes out and a flashback starts.
After the cutscene, when you gain control of the vessel, keep heading towards the island in the distance and steer the boat into the smaller craft that come up alongside you. Once the larger ship appears port-side, keep heading for the island while weaving back and forth to avoid the charges being lobbed at your ship. Nate can’t avoid them all, however - once you’re thrown from the wheelhouse, swim to the surface and avoid the oncoming enemy ship. Return to the boat where Sam is waiting and climb aboard, then take cover along the port-side rail and take down the attacking enemies while Sam repairs the engine. Once the engine is repaired, return to the helm and continue towards the island, avoid the large rocks jutting out of the sea. Eventually a cutscene will be triggered and the prologue will end.