Hi dudwasup,
You should study the Missions Manual and the Mission Editor Tutorial for information on sinking. Both can be downloaded from the top topic in the Missions board.
A mission is over when any player ship finishes sinking.
If you have a second player ship, you might be able to finish before the first ship goes all the way under, or hits bottom, but only if the first ship has no unfinished waypoints.
See Play > Missions "Disaster at Bergen"
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Regards,
Marty