Forts become available to attack during Sequence 3 Memory 3. The first one is story-based.
There are 6 forts. 3 in River Valley and 3 in North Atlantic. Their difficulty is shown by a number of dots on the fort icon on your map. 1 = easy, 2 = medium, 3 = hard. The list below shows each fort in each region and the difficulty (* asterisks instead of dots) River Valley
1. Fort La Croix * (story-based)
2. Fort Soleil **
3. Fort Blanc ***North Atlantic
4. Fort Louis *
5. Port La Joye **
6. Fort Baie Rouge ***
It is recommended that you greatly improve your ship before attacking the hard forts. Each fort requires attacking the defenses from your ship first, with mortar and cannons. I suggest taking out any ships that are defending the fort also. Keep moving to avoid enemy mortars. When fort defenses are eliminated, then you must dock and infiltrate the fort on foot. Kill key enemy personnel (other tasks could include sabotaging supplies).
If there are any ships surrounding the fort, incapacitate them first. If you are running low on health, you can board them in the middle of the fight and use them to repair the Morrigan. When you are done, you'll resume fighting the fort where you left off. This also works for any multi-ship fight in the game