* The very premise of the series scared some in a way ''Franchise/StarTrek'' never did. Whenever the base lost personnel and equipment, ''that's it''. There will be no replacements, and they are in growing danger of running out, especially since they apparently have no production facilities. At least in ''Series/StarTrekVoyager'', the ship had Neelix to rustle up supplies.
** Both played straight and partially averted in the ExpandedUniverse of novelizations and comics, where the Alphans were occasionally shown to have ''some'' limited mining and production facilities, but still had chronic supply problems. (Especially in season 2, where a crucial metal called "tiranium"(sic) always seemed to be in short supply.)
* The episode "Dragon's Domain", and that scene with the tentacled monster dragging screaming personnel into its mouth and spitting out dessicated, char-broiled, smoking corpses...
* An episode involving a pair of twins with some kind of voodoo power. The girl produced a very lifelike clay bust of Dr. Russel's head and proceeded to sink her fingers into the middle of the bust's face. The resulting scream of agony escaping from Dr. Russel's own fingers as she pressed them over her own face still can haunt nightmares.
* The fate of [[spoiler: Commissioner Simmonds]] in "Earthbound". After forcing his way aboard the vessel of some friendly aliens (who are, conveniently, headed for Earth) and who've agreed to take one Alphan passenger along for the ride (since they have a spare hibernation cubicle), [[spoiler: Simmonds awakes inside the glass cubicle only minutes into the voyage. Turns out, the aliens' suspended-animation process doesn't work on humans... and the aliens are asleep, and the cubicle can only be opened from the outside...]]
* The fate of [[spoiler: Dr. Rowland]] in "Death's Other Dominion".
* The titular "Troubled Spirit": [[spoiler: Dan Matteo's "ghost"]].