Whirl, after being an axe-crazy sociopath who caused Megatron's Start of Darkness and therefore is responsible for the entire Great War reveals that he was once a happy and successful watchmaker before the corrupt Senate drove him out of business, replacing his hands with bladed clamps to insure he'd never be able to do the job he loved ever again. Hardly condones his actions, really, but does go a long way to explaining them.
Fort Max completely breaking down when Rewind shows him footage of his torture from Garrus-9.
In issue 7 it's lightly implied that Krok's squad is either dead or went on without him and he's just mentally blocked that out, assuming their missing and constantly looking for them even though he'll never find them. That's pretty damn sad even for this series.
A subtle one but when Chromedome meets with Brainstorm he comments that he's Brainstorm's Only Friend. And Brainstorm doesn't correct him...
The Reveal that the Senator who befriended Orion Pax, defied his fellow corrupt senators, modified Orion to carry the Matrix, and ultimately surrendered himself to save Orion is Shockwave. Shockwave's current state is due to the Senate brainwashing and mutilating him. There's something inherently tragic and ironic about the fact that the two people who played the biggest role in making Orion into the heroic freedom-loving Optimus Prime, Megatron and Shockwave, became two of his worst foes.
Rodimus takes it very hard when he learns that Red Alert actually committed suicide, or attempted to, than suffering an attempt on his life by Cyclonus. Rodimus has made some bad calls during his tenure as captain, but this scene hits home what a Father to His Men he's really trying to be, taking it hard that he didn't see how much strain Red was under, despite having taken the time to talk to him about how worried he and everyone else was about him. You know how hard he's taking it as a personal failure on his part when they agree to put Red into storage until such time as they actually are in a position to help him.
Rodimus: See you later, Red. Promise.
Just about everything pertaining to Chromedome and Rewind in issue 12.
Tailgate coming clean to Cyclonus in issue 13 about lying about his entire backstory as a bomb disposal expert, a member of the Primal Vanguard, and crewmember on the Ark-1 because he's so frustrated that even after he went missing on the Mitteous Plateau-he was actually headed to the Ark to finish rinsing out its cooling chutes because he's a waste disposal 'bot-for six million years and no one ever noticed or cared, that he created this backstory so that someone might actually care about him. However, it turns into a Crowning Moment of Heartwarming soon after.
There's another one for Swerve at the end of issue 13 as well. Since the start of the series, Swerve has mentioned on several occasions that he's best friends with Blurr and that the two of them planned to open a bar together after the war (which they've both managed to do independently, with Blurr reopening Maccadam's on Cybertron, and Swerve's bar on the Lost Light). Issue 13 is Swerve sending a message to Blurr over his personal hailing frequency about the events on Hedonia, only for after nine hours of recording, Blaster tells him the transmission isn't going through. It's not going through because Swerve ISN'T friends with Blurr, and that they only actually met once, millions of years ago before the war at an autograph signing, and Swerve coming across as an obsessed Stalker with a Crush actually freaked Blurr out more than anything, causing him to give Swerve a fake hailing frequency (which Blaster even notes is too short to be real) when Swerve tells him they should open a bar together and begs him for Blurr's phone number and since then Swerve has clung to the belief that he and Blurr are best friends, when Blurr doesn't even seem to remember him at all. The last shot of Swerve standing alone quietly protesting that it is the right frequency is a pretty heartbreaking look at what's really going on behind that visor of his.
Pipes' death, specially after his little chat with Blaster, where he mentions that despite everything, he's ok and having a good time.
Once again, Chromedome and Rewind. Rewind realizing what Chromedome has done and not being sure he can ever forgive his Conjunx Endura. Rewind sacrificing himself so that Overlord can be jettisoned from the ship. Chromedome turning the Lost Light's cannons on the jettisoned cargo bay to save Rewind from Overlord. It's heart-rending.
Their final "goodbye" before the cell jettisoned, if you can call it that, was almost too much to bear. They can't hear each other through the glass, so we get shots from each of their perspectives as the countdown drones on in the background. There's this one panel of Rewind looking through the porthole, Chromedome's look of utter despair is reflected onto it, as Rewind says a goodbye Chromedome can't even hear.
Rewind: I'm sorry, Domey. I'm sorry things didn't work out.
Issue 16 continues the numerous Tearjerkers with Chromedome and Rewind. Chromedome basically is emotionally shattered by Rewind's death and barely shows any reactions at his funeral. We than get the incredibly disturbing reveal that Chromedome has had other Conjux Endura before Rewind who he's outlived and that every time that one dies, Chromedome basically erases his memory of them to keep the pain away. Not only that, we also learned that Chromedome has no innermost energon not because he was born dry (as he had said himself), but because he had made so many deathbed offerings that he had literally none to give. Brainstorm, in previous conversations, keeps trying to get him to stop erasing the memories of his previous Conjux Enduras but isn't successful until he shows Chromedome Rewind's last movie.
Also, Rewind's last message to Chromedome
Rewind:Your attention for a moment. This is Rewind, showing you edited footage from my database. I've probably got 0.8 seconds before game over, so hear me out. I've always been terrified that you'd die before I did, because you and me apart strikes me as intensely wrong. So promise me something. Be brave. And be strong. And keep going without me. And another thing: no more injecting. It will kill you. And remember: you deserve to be happy. The New Institute was the old you. You're a better person now—stubborn and frustrating, but wonderful. And to think, I will never see you again. One more thing—one last thing—because I don't say it enough: I love you.
At the same time as this Drift is exiled from the ship by Rodimus for his actions and has to leave all of his friends because of his actions. The other crew members are so shocked and angry that one of them even throws debris at Drift as he leaves. Ratchet is the only one who bothers to help Drift up after he's knocked down.
Drift has been a fairly unpopular character among the fandom and some the creators of the franchise from the beginning. Basically, he's been viewed as a nothing more than a stereotypical badass, fan-created Japanese samurai stereotyped character. It's sad that the only time Drift has ever elicited sympathy from anyone was when he took the fall for others, and that the last time we see him, he's still hated by just about everybody. Really brings his hard luck story full circle.
In issue 17, while preparing the team to take down to Luna-1's surface Rodimus confides to Ratchet that he knows Bumblebee and the other Autobots who stayed behind on Cybertron thought his quest was foolish, that Rodimus and his crew were just running away, and that the whole thing is some sort of joke to them.
Rodimus: But Rewind's not laughing. Hyperion's not laughing. Nor Animus. Nor Shock. People have died, Ratchet. People have died.
Ratchet breaks the news to Tailgate that he's suffering from cybercrosis and is going to die within the three next days.
Cyclonus' initial reaction seems to be disregard about Tailgate dying when he leaves their hab suite. Once outside, when he looks into a reflective surface, he raises his fist as if to smash it with a snarl. He stops. He just stops, with a broken and sad expression - as if thinking 'What's even the point?'. Instead, he drags his claws over his face, mutilating it.
The confrontation between Ultra Magnus/Minimus Ambus and Chief Justice Tyrest. Tyrest accuses Magnus of becoming a laughingstock due to his By-the-Book CopSuper OCD tendencies and is thus no longer worthy of carrying the title of Ultra Magnus, Duly Appointed Enforcer of the Tyrest Accord. Magnus/Ambus panics and begs Tyrest not to strip him of his title because being Ultra Magnus is his life, just before Tyrest presses a button on his staff, and the Ultra Magnus Powered Armor falls from Ambus' body. The last shot is of Ambus kneeling dejectedly on the ground, surrounded by the remains of his armor, holding the helmet in his hands. And then he gets thrown in prison to boot!
And than to top it off, Tyrest kicks Magnus while he's down saying that he's failed as an Enforcer, claims that Magnus is suffering a nervous breakdown, and shows off how he's being replaced with Star Saber. What a Jerkass.
Soundwave's pleading when the killswitch starts to affect Ravage.
Somebody help him!
The effects of the killswitch in general, which you would expect from an event that has seemingly random Cybertronians suddenly dropping with smoke coming out of their eyes and mouths. Soundwave panicking over Ravage, Starscream gasping Megatron's name, Red Alert quietly dying while in storage, Tarn's concern over Kaon, Fulcrum and Misfire wondering why there's no ship to pick them up, because their teammates are all effected, former friends Prowl and Chromedome dying together on opposite sides of the galaxy, completely unaware. And that's just the people we see.
What about THOSE WE DON'T SEE?
There's also First Aid lashing out at Ratchet, because Ratchet won't let him help try to fix Ambulon, which First Aid thinks is because of the bet he made with Pharma and his own inflated sense of pride, how he thinks Ratchet believes no one will ever be as good as him, which is why he's still Chief Medical Officer. And then it turns out the reason Ratchet won't let First Aid help is because Ambulon was dead before Pharma had even finished sawing him in half, and he's actually been rewiring Ambulon's corpse to turn it into a blaster (which is a whole new level of messed up right there) so they can escape. And even after all that, Ratchet still admits that First Aid had a point, and that if they survive, he'll step down and let First Aid take his place.
Tyrest tries to use Tailgate as a Human Shield to dissuade the away team from shooting him... at which Tailgate yells at Rodimus to shoot through him to take out Tyrest since he's dying already. Rodimus is understandably hesitant to say the least.
"I've only got a day and a half left! Now SHOOT HIM!
The end of the story arc ends up being rather bittersweet. Ambulon, Deftwing, and Dai Atlas are all dead and Tyrest and Star Saber escape. First Aid killed Pharma but he seems to be consumed with guilt over it and Rodimus had to sacrifice the Matrix map in order to stop the Killswitch, meaning the crew has no leads on finding the Knights Of Cybertron after everything they went through. And perhaps saddest of all, the hot spot the crew discovered won't reignite, meaning thousands of Cybertronions will never be born. Considering that by Prowl's calculations in the previous ongoing, Transformers are an increasingly endangered species that is edging closer and closer towards extinction, that's quite a blow.
When Rewind asks some of the crew if they're happy with their lives, Rung admits that no one has ever asked him how he felt before (And Rung is one of the oldest living Cybertronians we know about). The seemingly chipper and upbeat Drift doesn't say anything; he just remorsefully puts his face in his hand. Ouch.
Then Swerve says this:
"Everyone assumes that if you make jokes, you're happy. Why? Why is that?"
Blurr doesn't remember Swerve at all, and in fact finds him annoying.
In the six months since Dark Cybertron, Chromedome has fallen apart, and now spends all day in his quarters, listening to Rewinds last message, over and over.
When Trailcutter goes into medibay, it's shown that Ambulon's stuff is still in there; apparently neither Ratchet nor First Aid had the heart to get rid of it.
The final flashback to Megatron's trial has Rodimus sitting dejectedly in the dark because he caved and took Atomizer's list of the 89 people who voted against him staying as captain, and is seemingly crushed by the names on the list.
At the end of the trial, as part of the deal with Optimus to join the Lost Light, Megatron has to publicly denounce the Decepticon cause, declaring it a failed ideal and ordering any who still wore the badge to stand down. After he is done, he silently buries his face in his hands.
Ratchet points out to Rodimus that the voting records are fake because his name is not on the list. Rodimus' expression says it all.
In the end the Lost Light basically disintegrates, forcing the crew to abandon it. Given how they had largely come to view it as their home, that's a pretty big blow.
Riptide's anxiety whilst remembering the eight step program is instantly relatable for any academic strugglers.
Tailgate admitting that he's scared out of his mind to Cyclonus.
The whole concept of the MTOs, and their gradual degeneration into mass produced cannon fodder, is plenty messed up and sad. Skids in particular is angered with the process.
As more and more crewmembers disappear, Nautica breaks down and starts freaking out about how she may never see her friends from Caminus again.
Megatron and Ravage's heart-to-heart talk, when Megatron admits he sees himself as a monster. And the panel where Ravage has the most heartbroken look imaginable during all this.
During this conversation Megatron finally admits that he is old. And that his best days are long behind him, even without the Power Limiter fuel the Autobots are keeping him on. He finally admits to being what he really is; a tired old man full of regrets.
Megatron: Look at me Ravage. I'm old. Old and weak. Their poison makes me brittle, but even at full strength I'm long past my prime. My spark flickers when once it flared, and this body...oh, this nonsense body. It doesn't graft to the spark like the others. There's no purchase. No bite.
Nautica finding Brainstorm's corpse buried in the wreckage of his lab is pretty hard to read, especially considering just how close they had gotten over the past few months. Gets infinitely worse when he's revealed as the Decepticon's mole, and she is in desperate denial.
On your Lost Light, me and Domey... are we still strong?