re: Bad storylines in otherwise great shows (spoilers)

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Season 3 of Star Trek had a couple candidates;

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Back to the more broad topic of TOS - Season 3 - Spock's Brain is pretty poorly received, overall, although there were some decent Spock/McCoy banter moments. The plot was just irrecoverable. Nothing could have saved it.

The season was hampered by restricted budgets (compared to Seasons 1 and 2 - and consistently solid or better those first 2 seasons with few misses - Catspaw probably the worst of the 1st 2 seasons and it wasn't awful, particularly the guest star delivered an outstanding performance in a silly Halloween episode).

Season 3 - despite the budget woes, decreased Roddenberry participation, loss of Gene Coon midway through Season 2, etc., had some real gems - All Our Yesterdays, Day of the Dove, Spectre of the Gun, The Cloud Minders, Plato's Stepchildren, The Enterprise Incident, Elaan of Troyius, etc.

However, without question it had more than its fair share of bad episodes: Bad = Spock's Brain, And the Children Shall Lead Them, and Turnabout Intruder - probably 3 of the 4 worst (along with Catspaw from Season 2).