The plot summary is deliberately vague, so here are some examples of allegory in this very cool episode. They may be regarded as spoilers, but knowing them will make anticipation even better.
You say you want an example of allegory? A young Marine named Joseph (yes Joseph) Tenny is touring his new duty station with his pregnant wife Mary (they have been evicted because of some foul-up, though, and have no place to stay) when she goes into labor and has the baby in the Admiral's office. (The Admiral's middle name is Jethro.)
Meanwhile,three Arab lawyers in robes and headpieces just flew in from Kuwait to observe JAG's military justice system but are driving lost, all three with different interpretations of their only map, until they see the radio tower beacon on JAG's roof, and follow it, arriving just in time to give the Marine couple gifts from afar to celebrate their new boy, including a gold coin and a free apartment (one Arab confesses he owns 16 apartment buildings in Washington alone).
At the same moment, a C-130 Hercules full of Toys for Tots loses its instrumentation in heavy fog (yes, of course it's a foggy Christmas Eve –what did you expect?) and is guided for a landing by the hero in an F-14 with a red ID light on its nose blinking (yes Rudolph and "won't you guide my sleigh tonight" music etc.).
Those are just a few examples. The writers must have really loved doing this one. It works. It's not laugh-out-loud funny, it's more an-appreciative-smile humor.
Enjoy it!