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Welcome aboard the board matey.
In response to your question... The first ship to disable a flag ship (not first one to grapple it), would then load cannons with Grapple Hooks (option on far right of cannon screen), and fire into the green circles on the enemy flag ship. This connects the disabled ship to yours. Once "grappled" the captain of the ship will then have a "BOARD" button to initiate boarding the enemy ship when the crew is ready (there is a limited amount of time).
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