The Hidden Blade Assassin's Creed in Depth

http://youtu.be/-Zw45SQhAuU

Start off from the place shown in the video to board the ship. Quickly assassinate the captain (the guy at the helm who wears a hat, can't miss him) and make a mad dash for the "Jackdaw". You need to be fast to reach the helm before the timer runs out. Won't lie, I've cussed out the game for just barely not making it.

During the chase the "Royal fortune" can't be damaged due to the scripting of the mission, but once you reach a checkpoint one hit is enough to board the vessel. This is useful in a speedrun, especially if you don't have time to buy ship upgrades.