And Cliffjumper's death in the Bumblebee movie.

 

Not really, I was kind of expecting it, as I know that at least one Autobot will die in each film.

 

Yeah, but the way he died, being sliced right down the middle. I found it disturbing...

 

This was 8 year old me’s reaction to the TFP s2 finale.

 

8 years old for Transformers Prime Season 2? I'm 26 and I officially feel old.

 

No I watched TFP in 2014 so.....

 

Starscream's brutal beating in Cyberverse was waaaaaay more violent than any other beating, at some point it was hard to keep watching, I mean a quick death with a shoot is something, but literally torture Starscream and make him run for his life only to shoot him in tank mode and throw his body...
IDW deaths were brutal, maybe all of them, Last stand of the wreckers was hard to read too, especially at that Prowl moment
and also the Cosmic Rust ep in G1

 

The Throttlebots getting crushed into cubes was a particularly notable scene that I stumbled upon (I did find out a little while later that they lived and we're restored)

 

Cheetor almost getting his fluids sucked out, that was quite frightening.

 

Optimus Prime's death in the comics in issue 78 i think? When there's literally only a mangled torso left.
Dark Awakening terrified my when i was little.

Last Stand of the Wreckers and some of the DJD stuff was pretty grim too.

 

One may consider it tame compared to other things already mentioned, but Quintesson Arc of Cyberverse. After being used to the (mostly) lighthearted tone of the show, Quintesson Arc looks grim both literally and figuratively with Quintesson's Matrix-like scheme. And, eventually, the parade scene itself becomes kinda unnerving, especially as you learn that Quintessons essentially drink their sparks during that parade.
The most disturbing thing for me were the Quintessons themselves. Initially I assumed the prosecutors were all the Quintessons, and they're rather unnerving as they don't communicate verbally and look like something eldritch. But then it was revealed that there's the Scientist and the Judge. The Scientist is just plain old creepy, especially when he gets his tentacles on Soundwave. His real form, short its appearance may be, is actually visceral and disturbing. Good thing Wheeljack got rid of him, though the act itself is kinda "squick" business as well.
And the Judge is... eldritch-ly creepy with their five faces. Again, it was the first time I saw these guys. And they're disturbing. Especially Chaos and Death, though others don't help at all. Especially when the Judge is framed with black-and-red of Quintesson tech. In hindsight I think they're more disturbing than G1 Quintessons.

They're creepy.

 

I mean, even if the Nebulons are re-engineered into cyborgs who can transform, there's still the question of why, exactly, an engine needs to be sapient. Or disconnectable. Or mounted out on the surface of a vehicle which will probably be in battle quite a lot.

Sure, in the Marvel comics there was at least something of a reason for the process - it allowed certain Nebulons to in turn allow individual Transformers to operate on Nebulos without running out of fuel, so it was as much ideological as anything. The only reason I can think of for the Nebulons to insist that the engines contain a fully sapient Nebulon at all, much less one which wasn't safely attached under the Transformer's outer plating, was that they desperately wanted to retain the ability to simply disconnect and run away if the Transformer turned out to be doing anything the specific binary-bonded Nebulon didn't like. Pure suspicion.

And, you know, presumably the various Nebulons couldn't simply be intimidated into converting fuel. "Make me lunch or I'll transform you into a flesh and metal pretzel!"