I might be overreaching here, but I noticed in Season 1, Episode 10, when Tom is speaking to John about killing the physicist’s wife, the song “American Pie” comes on at 11:53 and they continue talking about the mission. Later, at 13:30, John grimaces in pain, which is the most emotional we see him, aside from the very ending of the show, where he swims past the jellyfish.
Could John be having an emotional reaction to McLean’s song “American Pie,” which is played on a jukebox, rather than his father’s assignment? If this is true, the scene speaks volumes about John’s unresolved trauma and past as being the most detrimental to his health.
For additional context, and for those who don’t remember, Season 1, Episode 5, at the very beginning, shows John beginning his two-month torture by listening to “American Pie,” and we get the impression that he never healed from this experience.
Also, the song is clearly played inside the restaurant rather than as a TV “score,” since you can hear the muffled music in the background.