Sam and Callen are trapped in the submarine. The terrorists cut off their oxygen supply which forces the agents to find a way to force the sub to the surface. They figure out that the submarine is headed towards San Diego. Their guess is that it's going to be used as a bomb to take out an nuclear powered aircraft carrier. The terrorists are on a suicide mission and now so are Sam and Callen.
The NCIS agents decide they will sacrifice their own lives if it means protecting the targeted people and preventing a nuclear disaster.
The rest of the NCIS LA team searches for clues to what happened to the sub. Kensi finds a receipt for fertilizer and realizes that the sub is being used as a bomb. Hetty delays her trip to DC to return to NCIS.
Sam and Callen set a fire and breach the hull to force the submarine off course. The terrorists finally are forced to open the door where they find Sam and Callen waiting for them. The agents take out the terrorists.
The Navy authorizes a bomb launch to take out the submarine.
Sam and Callen escape the submarine just in time to avoid being killed by the Navy's strike on the sub.
Kensi and Deeks spot their fellow agents in the water.