Sic Semper Tyrannis
This story missions launches immediately after completing 'No Chains Too Thick.'
This time you're going after the local Big Bad – Rufio.
Follow Amunet to his fleet, but wind up in a village being put to the torch.
Kill all hostiles. This is actually a pretty easy fight- in the chaos and dark you can assassinate and refill adrenaline many times, and Amunet remains a quick and capable fighter.
When the last raider has fallen, grab a boat and make for Rufio's mooring.
Like the beach, this place looks tougher than it is. You can sneak-kill your way in, but you can also just make straight for Rufio's boat and kill the handful of guards there. You will likely be spotted by guards on nearby ships, but they can't actually do much to you. However you proceed, Rufio is inside his tent, on the center ship.
Kill and kill-confirm him to complete the mission, and automatically launch a final story mission – 'The Greater Good.'
Note that there is a treasure beneath Rufio's ship, amongst a little octopus garden of bodies.