The scene when the submarine emerges from underwater towards the end of the episode is taken from The Hunt for Red October (1990).
Lt. Steven Albright returns later in the series, though not at Christmas as his conversation with Natalie would seem to suggest. He shows up in the concluding two-parter of the series.
The murder weapon looks like a Luger P08, which is a German pistol used during WWI and WWII. No explanation is provided as to why it would be in use on a 20th century US submarine.