Ok, it looks like this is starting to get somewhere, and this is a good thing.
I will try to explain this premise further.

1. This vessel is under the command of the U. S. Navy?s Atlantic Submarine Command.
2. Its purpose is for scientific research when not called to fight terrorism and piracy.
3. The Crew is a mixture of personnel from various countries friendly to the United States.
4. The civilian staff is also from various countries.
5. The reason why Dr. Samantha Ryan is on board the vessel is study how the crew and staff work together. After all, there are many politics involved in this and we do not need an international incident.

Now, getting back to her ex husband.

While out to sea, the skipper orders that the shake down starts. Everybody is doing his or her jobs and such. However, during a systems check on the computer, a yet unknown virus activates and starts to cause minor problems. These problems are not considered serious because it is a new vessel. However, when a diagnostic is done, an embedded video begins playing on all of the monitors. Dr. Ryan, being on the bridge when this happens, was talking to the skipper on the bridge. She sees the video playing, and recognizes the person speaking as her ex-husband. He starts by saying, Hello, Samantha. Remember me?? He then continues about what happened since his release from prison and the threats start. When he finishes, all hell breaks loose with major system wide problems.

The skipper calls a meeting so Dr. Ryan can explain, What the hell is going on and who the hell is that guy?? – Skipper.

Being the Director of PsyOps, a division of the Department of Defense, she has to use her skills to help stop her husband and save everybody on board the sub. As I suggested earlier, she is the female version of Sherlock Holms while her ex is James Moriarty.

So, by adjusting your example, it would be rendered as the following.

When the head of the U.S. Navy Psy Ops division discovers her vengeful ex has planted a computer virus on a Submarine she must (insert what she MUST do, in essence, her GOAL?), before (insert worst case scenario?the STAKES) happens??

Does this help clear the confusion?