The first thing that came to mind is one of the early Gold Keys where the Enterprise discovers a planet of sentient plant life and then carpet bombs the entire planet.
The spores of which turned every living thing into giant, man-eating plant monsters. And in the whacky context of the Gold Key universe, the spores were already travelling through space and thus a risk to every inhabited planet.
During the honeymoon of Nancy Bryce and Konom the Klingon, the Enterprise crew are drawn into the Circles of Hell (as described in "Dante's Inferno") when a sleeping, telepathic crewman causes his shipmates to share hallucinations. Spock uses a mind-meld to restore sanity to the ship - and then Ensign Bearclaw plunges a knife into Kirk's chest. (Issues #51-52, Series I, DC.)
That was the very first issue. I wouldn't call it "dark" in-story, though, since by the morality intended by the writer, the characters were performing an unambiguously heroic act. It's only in retrospect, filtered through a knowledge of Star Trek's moral baseline that the writer of that comic didn't yet have, that it looks shocking. Probably a list of the darkest Trek comic stories would include Peter David's work (including the issues Therin just mentioned). He gets perceived as a comedic writer, but the humor in his work is balanced by some pretty dark, disquieting plots and themes.
I remember Marvel's Star Trek: Operation Assimilation being very dark. I should dig that up and read it; it's the only Star Trek work by Paul Jenkins.
DC #37 (first run), can't remember the name of the story, but it was about a terrorist trying to destroy the 1701-A on her maiden voyage. By Len Wein and Curt Swan, IIRC. I'd also pick Star Trek Annual #2, "The Final Mission" where the Enterprise returns to Talos IV.
I thought the Discovery miniseries "Succession", Spoiler set in the Mirror Universe, had some nice dark moments, more so than the also recent TNG Mirror Universe books-Mirror Broken, Through the Mirror, and Terra Incognita. I also thought the Discovery miniseries "The Light of Kahless" had some dark moments as well.
#37 Apr 1987 "Choices" Following Kirk's demotion to captain and reassignment to the Enterprise, his fellow officers consider their future and rejoin him for new adventures. A religious fanatic attempts to destroy the newly refitted Enterprise, but is thwarted by Spock. Stardate 8925.2. The first post-ST IV comic and the reintroduction of Arex and M'Ress from TAS. Thanks Mark Martinez: https://www.startrekcomics.info