During the last naval battle of Episode 3 Sequence 1, there are two triggers: one for spawning the second wave of Washington's fleet, the other for triggering the cutscene leading into the setpiece where Ratonhake'ton crashes the Aquila into the Man 'o War. I have played this mission dozens of times, and for the life of me I cannot figure out what causes them to trigger. It's not killing a certain number of ships, because destroying 80% of Washington's fleet is an optional objective, and it's not retreating, because it's an arena fight, and leaving the area causes a desync.

If anyone can give me a hand, I will love you forever :D

Considering optional objective it seems to be just on fixed timer - you have a certain time to sink as many ships as you can and after that you get the checkpoint.