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troperville

Whirl talking to several leftover Sweep carcasses which he had pinned to a wall inside a shabby structure out in Cybertron's wastelands, and apparently mutilating them as a disturbing method of stress relief. And apparently he did this because he was frustrated with the NAI Ls(Non-Aligned Indigenous Life-forms aka Neutral Transformers) and having been kicked out of the Wreckers. When he had his fun, Whirl doused the ruins with (energon) fuel and bid a very creepy thank you and farewell to the remains, planning to burn it all�quite possibly, himself included...until Cyclonus accidentally interrupted everything.
Tailgate. Stuck in a tunnel in the middle of nowhere, with both his legs completely destroyed, and no one coming to find or rescue him. FOR SIX MILLION YEARS!!
When The Lost Light suffered a catastrophic accident which involved an explosion in its quantum engines that forces the ship to quantum jump before its preparation is complete, it is hurled off some far corner of the galaxy, and a fifth of the ship's crew is sucked out into space through the breach , burning up as they entered atmosphere.
The very first issue has the extremely creepy message from the future, trying to warn the crew of the Lost Light not to leave Cybertron.

MTMTE Issue 2:

Issue #2 features Skids warping in over the same planet the Lost Light landed on, with no memory of his most recent history, an inhibitor claw strapped to his back, and a very definite feeling that he is fleeing from something. He thinks he must have gotten away, completely missing the writing on the wall behind him that reads "YOU HAVEN'T ESCAPED. THEY'RE ALL AROUND YOU." It turns out the shuttle he's on is in fact three giant sword-wielding robots (which can breathe fire, by the way) that end up pursuing him across the planet, all the while repeating "Nineteen-eighty-four..." over and over again. They will NEVER, EVER STOP until they have captured what they need to capture.
- For the record, those Giant robots with swords are named Legislators as they were given that name in the concept sketches of MTMTE.
Red Alert telling Rodimus alarmingly that There is a Sparkeater aboard the Lost Light. Beside him, one of the Duobots, more specifically Shock, is dead with his mouth hanging open and a hole in his chest.

How the Sparkeater kills the duobot Shock. It immobilizes Shock and forces him to regurgitate his own brain capsule, killing him and causing his spark to emerge for the Sparkeater to devour.
The Sparkeater. Enough said. It consumes Cybertronian sparks and hunts down Cybertronians, specifically for those who have the "brightest spark", and it will NEVER, EVER STOP until it finds what it wants and consumes the "brightest spark". Combine the creepiness and design concept of the Xenomorphs from Aliens with the determination of a Terminator when pursuing a chosen target, that is what a Sparkeater IS.
- Due to the lack of general knowledge about them and the myths that have sprung up around them, they are sometimes also known as Cybervores, Soulsnatchers, and The Nightmare with a Thousand Names. The sheer mention of them can strike fear even in the most battle-hardened of warriors.
- and here is a traditional Cybertronian Rhyme about Sparkeaters.
  "Nickel, iron, cobalt, chrome,
  He'll eat your soul,
  Turn your spark to stone,
  Nickel, iron, cobalt, chrome,
  Run, little robot, run away home."
  �Traditional Cybertronian rhyme

First Aid creates an Apocalypse log that chronicles the hopeless situation at Delphi, the medical center. The bots there are all infected with a disease which causes their internal organs to liquify and come out their eyes. In other words, they cry themselves to death.

Fortress Maximus killing Sonic and Boom.
Pharma standing in a room filled with hundreds of Transformation cogs. HOLY PRIMUS. And that grin he has on his face was freaking scary.

What Fortress Maximus had to endure, and eventually what he became.
There's also Overlord's torture of Fort Max, which is shown-graphically-in issue #6, both in flashback and in video form by Rewind to distract Maximus after he takes Rung and Whirl hostage. Being shown footage of his own horrific torture, including Overlord's Energon-splattered face is horrifying enough that it causes him to fall to the ground crying.
The sheer fact that Red Alert discovering a phase sixer Decepticon, or more accurately, OVERLORD is restrained within a hidden chamber at the bottom of the ship when there should have been empty space.

The Decepticon squad finds a large ship, and in that ship are some very horrific things. Brain Modules are found, along with deformed protoforms (the equivalent of aborted fetuses). There is also a room with skin on it which has bled into the fuel supply. The crowning gem is Grimlock, the autobot notorious for killing Decepticons.
Vos: "Wear my faaace."
Tesarus: "Stop struggling and come inside Flywheels."

Shockwave's origin, told in issue 11.
The manner by which Red Alert chose to commit suicide; removing his own head. Apparently, it's rather easy to do if you're old enough.
The Institute. Full-stop.

The look on Swerve's face after he accidentally shoots it off in battle with Decepticons. It's...not pretty, considering you can see his robotic skull and optic hanging out.

Imagine you're an Autobot onboard the Lost Light. Just a regular, average grunt, nobody important, who's tagging along on Rodimus' quest for whatever reason. You've survived thus far, and you've just had some much-needed shore-leave on Hedonia, and now you're going about your duties on the ship, or maybe you're off-duty and having a drink at Swerve's, or recharging quietly in your hab-suite, something like that. Just a normal day on the ship. Then alarms start blasting, shots are being fired and people are screaming because Overlord, one of the most powerful, ruthless, and sadistic Decepticons to ever exist, capable of razing entire worlds on his own is suddenly inside the ship and he's killing everyone. No one has any idea how he got into the ship, where he came from, how he got repaired, nothing. He's just suddenly there and there's a good chance you're about to die. Even worse if you find out some of your crewmates actually did know he was on the ship but never told anyone or had security measures in place in case he got out.
How Overlord kills Pipes when the latter accidentally bumps into the former while on his way to watch Rewind's movie. BY STOMPING ON HIM UNTIL HE'S A MESS OF A RUIN.

Though it's a lot more low key than previous examples, there's something extremely disturbing about the reveal that Chromedome has erased his own memories of past lovers to avoid the emotional pain.