At the end of sequence 2 / beginning of sequence 3, you've obtained your own ship, the Jackdaw. The first task you have is sailing to a small Island; this Island (Abaco Island) has but a few activities to complete, and the storyline takes you straight to it.
At Abaco Island, you need to do the following activities:
1 viewpoint to synchronise
1 chest to open
3 animus fragments to collect
2 secrets to find (the secrets on this island are a treasure map obtained from a dead pirate, and a letter in a bottle)
All of these activities show up on your map when you synchronise from the viewpoint on the Island, so it's a case of walking up to them and completing the action - or in the case of the animus fragments, finding a way to climb up to them.
You can find your progress in the "progress tracker" option of the pause menu. you'll find the locations under either major locations or secondary locations, obviously the secondary locations should take less time than the major locations. Things like viewpoints and assassination contracts don't show up on the progress tracker - it only shows collectibles. Since these viewpoints, contracts and such are listed as "side activities", and the symbol on your map for the island doesn't turn gold unless you've done the side activities too; I believe that you need to do all side activities on an island too before you'd get the trophy. I did the viewpoint on Abaco Island before doing the collectibles so I can't say for sure; if anyone gets the trophy with certain side activities not completed just post a comment and I'll update the solution. You can find a list of all side activities by highlighting the symbol of the place on your map, but only if you're currently somewhere else. Somewhere else can also be a few meters into the sea. I found a treasure map for a treasure on Abaco Island after getting the trophy. This means that treasure hidden on an island doesn't count towards its completion percentage; only maps found on the island do.