The San Ignacio Wreck in Assassin's Creed 4: Black Flag is the only mandatory Diving site you will encounter. You can find the Elite Hull Upgrade hidden in the chests in the depths.
Walkthrough[edit]
Go straight forward from the Diving Bell. Dive down to the sea floor and collect the first chest. Now swim over to the right, toward the next part of the wreck to the North. Take care to avoid the jellyfish. Inside the hull of the bow you will find the next chest. After that swim up the mast to collect the first of three Animus Fragments. From there swim to the right-hand side of the hull section to the North. Inside there you will find the third chest of the dive (completing the first optional objective). Now head for the glowing section of the hull to the South of you. use the nearby Air Barrel if you are at less than half air.
Swim on down tot he chest pinned underneath the beam of wood. Interact with it to cause the wall nearby to collapse. Now you need to head into the newly revealed cave. You cannot go back the same way. Swim into the cave that has opened up in front of you. Keep going through until you reach the first air pocket. Surface and refill your breath. Swim over to the Western side of the cavern then dive down again into the tunnel. When the tunnel opens up Edward will get swept up in a strong current. Weave around the various rock formations that will loom in front of you. Once the current lets go you only have a short distance to go to make it out of the cave.
When you make it out of the cave then find the nearest Air barrel. Edward should have fair need of it. This is where you also first see a shark. Keep low and go for the Air barrel then duck into the seaweed patch.
Watch the nearby shark and wait for it to turn away from you. Head to the Northeast to make it over to the next section of hull and collect the Animus Fragment inside. Head to the far end of the wreckage. Go to the Northeast to reach the far treasure chest first. After that go to the diving bell and replenish your air.
Next duck into the seaweed patches on the sea bed. Move over to the next chest and collect it. From there go to the Northwest and go into the next hull. You will find the final Animus Fragment sitting outside a section of hull nearby the final chest. Go for each of them in turn, being mindful of the sharks. After that just make your way carefully over to the Diving Bell and finish out this dive.
