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I've found that the green circles come up once the sails have been shot down so that the ship can't sail away and the hull is damaged. Switch from the cannon shot to the grappling hooks (right click or use the scroll wheel on your mouse), and aim for the green circles. If your shot is successful, you'll see a rope slung between your ship and the enemy ship. The program will pull the ships closer. Exit your stance at the cannon and go to the railing like you want to exit the ship. When the ship is close enough, the program will indicate "Press Control to board enemy ship".
Once you're on board, a variety of things could happen. Fight the soldiers. Take over the helm (although once a soldier got back to the helm after I left it, and I was stranded on this enemy ship, unable to exit the ship or take back over the helm with soldiers that kept respawning ). Or get hit with a bug. We were most successful when we killed off all the enemy crew. We were immediately transferred back to our ship (reverse rope move) and the enemy ship sunk.
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