Speak with the scout and follow him to the camp to speak with the commander.
Optional objective: Cross Charlestown without taking damage.
When the cutscene ends, you will receive a mission of reaching the enemy ship. For that however, you will have to cross a bombarded town.
In order to avoid damage, go maximally to the right after reaching the main road and stick to the edge of the location (grey Animus wall).
That way you will reach the harbor and from there will be able to swim to the marked point.
Optional objective: Air assassinate a Grenadier.
Optional objective: Remain undetected while on ships.
Optional objective: Completed all the constraints in one playthrough.
After you reach the target, you will receive a task of blowing up the two nearby ships and two additional objectives: air assassinating a grenadier and remaining unnoticed by the crew of the ships. Start off by swimming around the ship on the left and grab the edge of the ship. Hanging from the deck, you need to eliminate two patrolling soldiers.
If they don't approach you close enough for you to throw them into the ocean, get aboard the ship for a second and leave it right afterwards. That way you will draw them to the edge of the ship. Just remember to kill the enemies one at a time when the others aren't looking.
With both enemies eliminated, approach the marked spot and press the hold down the interaction button so that Connor plants the explosive charge.
Leave the ship before the bomb explodes and swim to the second one.
Onboard you can find a characteristic grenadier which you can recognize by his characteristic hat. Don't kill him right now.
Instead, eliminate the enemy walking nearby the edge and the soldier standing by the end of the ship. Kill the latter one when the grenadier faces the other direction.
With both enemies dead, climb the pile of crate by the mast and kill the grenadier from there. That way you will complete the optional objective.
Now you can plant the charge and run to the water.
After the explosion, return to the wreck and climb the mast to change the flag.
After reaching the shore, the mission will end.