Well, they took care of the sub a full episode earlier than I expected. It sets up a season finale along different lines than the typical "final showdown".
Two stories running. The A story was the Nathan James fighting the sub, and it was well executed. It took some nods from the classic "The Enemy Below" and added a twist or two. Well paced and they way they finally defeated the Ramsey's with no sonar (it was damaged previously) was clever, as Chandler took advantage of the relative inexperience of Ramsey as a sub commander and baited him into a fatal error.
The B story had to do with the medical teams, which had been put ashore with the commandos to safeguard them earlier when they realized the James had to fight the sub to survive. They both started spreading the now contagious cure and took out a SSM (Surface to Surface Missile) site the Ramsey's had set up as insurance.
More people got shot up including the XO, but no deaths (except the Ramsey's and the sub crew of course). Really an action story episode flat out.