You will have to follow a gunship over rough area. You need to watch out for watchtowers and steer clear of them. Already after you begin, there will be the first tower. Steer to the left to bypass it. Right afterwards, there will be another one, and two more, next to each other. You will bypass all of them easily if you keep to the left branch.
There is no way to bypass the next two towers. Jump out of the Jackdaw and run up to the alarm to disable it. There will only be the regular soldiers here so, you can cut through using force (this mission has no time limit on it). Once you damage the bell, return to your ship, which will in a moment stop nearby.
Ahead, there will be no additional obstacles anymore, it is enough to sail ahead. A bit further, you will have to leave the Jackdaw again and go ahead on foot.
OPTIONAL OBJECTIVE- use sleeping darts on three crocodiles
OPTIONAL OBJECTIVE- skin a crocodile
Right at the first passage, you should encounter the crocodile shown in the screenshot. You especially need to watch out in this part of the map. Put it to sleep and skin it. Then, run ahead while still keeping to the boat.
Here, you do not need to worry about the boat itself too much, because it should not spot you. Additionally, every now and then, it will stop and let you make up for the lost meters. The crocodiles are a bane here and you need to be extra careful about them, the best idea is to initiate the eagle vision frequently. Also, you need to remember to finish off a crocodile after you put it to sleep. If you don't it will soon wake up and pose a threat again. If one manages to come close to you, you will have to drive it away by tapping quickly on the buttons displayed on the screen, during a dynamic event. Note, however, that if you drive one away, it will soon come back so, you should hide in the meanwhile and prepare the blowgun.
A bit ahead, the boat will sail past ruins with a multitude of soldiers inside. Make your way onto the top and jump over columns, above the soldiers' heads.
In the next part, you will have to eavesdrop on a conversation. Follow the two soldiers and hide behind any available covers.
Finally, you will have to kill the captain This one is a very dynamic sequence including a series of explosions and other adornments but, basically it will be no different than the other chases that you took part in. Simply, run after the captain and ignore all that is going on around you. Even if the bridge is blown up, you will still be able to run over it. Simply, run for the captain. Once you are close, knock him down and finish off quickly, which will conclude this mission.