In a story not unfamiliar to Star Trek, a superior intelligence (or in this case, unseen technology) plays god to an unsuspecting tribe of primitive humanoids. The titular "Apple" references the conceptual clothing of this society: Genesis.
This Space-Eden uses all its biblical imagery to flesh out the aesthetic experience -- including the serpent's visage for the ruling deity -- retaining very little of the thematic substance. The parallel reference with the most dramatic promise lies in Kirk's own struggle to blindly follow his own orders, as the natives follow theirs, at the expense of his crew. This conflict, however, is relegated to two mentions in dialogue.
There is a compelling conceit hidden at this episode's heart, justifying its Biblical namesake. The primitive society in question is completely stagnate. They neither age nor progress. Nor do they love. Their freedom compromised by blind faith. They are removed from time in an artificial Eden as the mythological Adam and Eve's experience references the essential human condition in the realm of space and time. Life, love, growth, and freedom stem from the inherent pairs of opposites accepted with the bite of the fruit of the Tree of the Knowledge of Good and Evil. Ought we offer that bite to those in an Eden of artifice, as Kirk and Co. ultimately do?
Unfortunately for the overall strength of the episode, these themes are pushed aside as set dressing when Kirk, speaking for the storytellers, brashly states:
"I think this philosophical argument can wait until our ship's out of danger."
"I think this philosophical argument can wait until our ship's out of danger."
Where stronger Star Trek might use this conceptual base to explore and further define the depths of humanity's core attributes, here it is given only the faintest connective importance to the other elements of the episode. Namely, an ultimately unexplained and thematically irrelevant threat to our hero's starship.
As artificially created as the Eden depicted, the tension of the orbiting Enterprise's imminent peril is an inappropriately executed contrivance. So too is the superficial reuse of the Amok Time musical theme to represent the "tribal" society. Both play on more effective prior use.
Aside from the canonically interesting early-mentions of the Prime Directive and Saucer-Separation, as well as several comedic moments spawning from the now well-established character types, there is little true drama or theme to be gleaned from the dull, unpolished shine of "The Apple."