Subplots and episodes incorporate themes of institutional prejudice, such as lingering Federation biases against genetically modified Illyrians (carried from prior seasons but echoed in character arcs), and one installment questions Starfleet's role as potential imperial colonizer imposing laws and doctrines. The season includes farcical elements in episodes like 'Four-and-a-Half Vulcans' that drew accusations of mishandling neurodivergence and other sensitivities.

Significant audience backlash labels the show 'woke,' citing misandry, sentimentalism, and crew composition, with rumors of Paramount reshoots to excise excessive progressive content causing delays. These elements influence character dynamics and select storylines but remain secondary to the core premise of Gorn conflicts, exploration adventures, romance, and mystery, without race- or gender-swapping established canon figures or centering the narrative on identity politics.