- Moral Event Horizon: If Sunad hadn't already crossed it for wanting to kill John Doe (and possibly having already killed his comrades) for supposedly being a threat, then trying to murder everyone on the Enterprise definitely puts him over the edge.
- Nightmare Fuel: John Doe's appearance when he's first found by the Enterprise away team. More immediately apparent than the loss of his left arm is that he's received extreme facial trauma, with his brain exposed and skin ripped away from his cheek, exposing his back teeth. One wonders how that bit of makeup SFX made it past Paramount censors...
- Possibly because of the low quality of the original TV-standard recording, as remasters show the trauma on his face more clearly.
- Padding: The two-minute scene of Picard and Data trying to determine where exactly John Doe came from is one of the more notorious Techno Babble scenes in the show's history, with the two doing nothing but sitting on the bridge and spewing out meaningless jargon.
- The scene is rather long, but at least it includes a decent example of Shown Their Work, using a downloaded star chart and the pulsars shown within to trace John Doe's ship back to its destination. (Pulsars have a very stable "flash" frequency, which makes them useful for triangulating positions in space. The Pioneer and Voyager probes included a map that depicted Earth's location relative to over a dozen pulsars.)
- Special Effects Failure: At the end of the episode, John Doe is transformed into a glowing yellow energy being... which looks like a person wearing a glowing morphsuit. The HD remaster really doesn't help, turning what was originally a hit-or-miss effect on first transmission into a thousand-yard miss.
- What Do You Mean, It's Not Symbolic?: For some, this episode is oozing religious references. It helps this episode is called Transfigurations.
YMMV / Star Trek: The Next Generation S3E25 "Transfigurations"