For me, the most disturbing scene in all of Star Trek is the DS9 episode where the female vedek friend of Kira's hangs herself in order to prove a point to Kira that the Dominion is evil and should not be bargained with. When I saw her feet dangling and her hat falling to the floor, I literally felt sick. I have shivers just writing about it.
Another disturbing scene is Odo's flashback to when he was security chief on Terok Nor and watched the execution of the three Bajoran workers.
Another disturbing scene is Odo's flashback to when he was security chief on Terok Nor and watched the execution of the three Bajoran workers.