Things that could happen at sea:
- A terrible storm which causes damage to the boat which must be repaired.
- Someone goes overboard.
- Someone from another boat goes overboard and the pirate ship crew rescues them.
- A run in with another pirate ship, maybe the other pirate ship tries to take over your pirate ship.
- A mutiny.
- The law catches up with them and they risk trial.

Umm... that's all I can think of just now. Are any of those any use to you?