"Shipyard Infiltration" is awarded for completing the second chapter of the game. You'll spend a good chunk of time running from a hail of helicopter gunfire, so keep moving and look for explosive tanks if you feel like you've reached a dead end.
At the end of the level, you will jump onto a boat and be boarded three times to engage in hand-to-hand combat. The final battle is a boss-fight type of encounter, in which you will appear to lose even if you win. As the cinematic plays with Bourne hanging off the side of the boat, the Achievement will unlock.