This sounds a lot like "Under Siege" (the Steven Segal movie). A few recommendations, there would never be just one Navy SEAL on a ship. There would be at least two to operate their Seal Delivery Vehicle (mini wet sub) that they usually attach to subs. Also, the first thing the Captain would do (if he knew the guy was a SEAL) would be to get him on his side or to get rid of him before launching his operation. You never want to leave a lose end like that so you deal with everything standing in your way first.
It could be a good story as long as you do the research to keep it grounded in reality a little more.
It could be a good story as long as you do the research to keep it grounded in reality a little more.