Any time a soldier dies, it's another dose of hopelessness to an already bleak situation; even worse when the person in question received just enough development to make people care about them.
The first chapter when the Survey Corps came back, and the mother was given her son's arm. The commanding officer remains solemn but calm when the mother asks for her son. But then it quickly shatters when the mother asks if her son was useful. His gut reaction is to say yes to comfort her, but he immediately confesses that the excursion was a complete failure, blaming his own incompetence for the lives lost, and saying all of their missions in the past hundred years have been a failure, losing men with no results. It really sets the tone of the series.
The first ending of the anime can be this after seeing the backstory of how Eren and Mikasa first met.
After their mother spends the last few minutes desperately trying to convince Eren and Mikasa to leave her behind before all three of them get eaten by the oncoming Titan, she first seems relieved that at least her children will be safe as Hannes carries them away. Suddenly though, she has a flashback to how happy they were as a family. Her last tearful words before the Smiling Titan picks her up are "...Please don't leave me." She covers her mouth so that the children can't hear.
It was pretty sad seeing Armin crying over his grandfather's death, who was the only one looking after him as well as Eren and Mikasa. In order to solve a food shortage crisis, the central government drafted 250,000 refugees, including Armin's grandfather, to reclaim Wall Maria from the Titans. Only 100 people survived. The last thing that he gave to Armin before he departed was his straw hat, and we see Armin crying into it after receiving news that he did not survive the campaign.
Early on in the barracks, Armin talks about why he wants to become a soldier instead of living in the landfill: despite being physically weak and utterly lacking in confidence, he just can't sit there and do nothing. And then he goes on his first real mission, and is so terrified that he freezes on the spot, wondering how in the hell he can just sit there, watching his friends be eaten. He's just plain unable to move, even when a Titan picks him up and drops him down its throat.
In the flashback to Mikasa's past, she was living happily with her parents before they were killed right in front her and she was kidnapped. After she was saved, she says, "I need to go home, where should I go? Now I have nowhere, nowhere left to go."
Hannah and Franz, whom Eren said seemed like a couple. In the Battle of Trost, Hannah is shown giving CPR to Franz. Armin finds her, pauses with a solemn look on his face, and tells her to stop. The panel pans out and we see Franz cut in half. And Hannah just keeps on trying to resuscitate him...
The scene is much more powerful in the anime — you can hear Hannah's panic and see her slowly crumbling mental state, as well as an already distraught Armin trying to get Hannah to see what had happened.
In Episode 7, one of the soldiers trapped in a building surrounded by Titans decides it is better to die than be eaten, and kills himself. While this is upsetting by itself (especially for the people with him), it's made even worse by the fact that just a little while afterwards, the other trainees make it to the building to help them, and Mikasa, Connie, and Armin bring Titan Eren with them to take out all the Titans — meaning that if he had waited a bit longer, he would have been saved.
Mikasa's struggle at the end of Episode 7, which doubles as an Awesome Moment. Believing Eren's dead, she feels she has nothing left to live for, and resigns herself to be eaten by the titans. However, her body moves on its own, and she realizes she wants to keep on living just to treasure Eren's memory. The beautiful music from "Counter Attack Mankind", the teary VO performance and great visuals seal the deal for one of the most memorable moments in the anime.
Armin and Mikasa have the exact same reaction to Eren being devoured. They lose control of their bodies; the difference is that Armin is too horrified by the grim reality of what he knows is happening to move; Mikasa is so detached she can't suppress her survival instinct and razor-sharp reflexes enough to let herself be eaten. It serves both as an elegant illustration of their character types, and as a heartbreaking show of closeness.
In Chapter 10, while Eren was in the Titan's stomach, he was thinking of his life and why he lost everything. It gets better.
Additionally, a random female soldier inside the Titan's stomach is still alive and cries out for her mother in her last moments. It's even sadder in the anime.
Even sadder in the anime: they added a flashback of Eren as a child, smiling happily with his mother, and you can his voice trembling with despair and fury as he wonders why they have to suffer like this and vows to kill the Titans with his hands. The music in the background doesn't help.
During Episode 12 after Eren can't control his Titan form and it appears that the mission has failed one of the soldiers says that they should fall back, but Ian refuses to, still wanting to attempt to carry out the operation despite all evidence that it will fail. Why? Because the situation Humanity is in is so bad that throwing thousands of lives away at opportunities that have a slim chance of working at the very best is a practical option. It says a lot about the conflict with the Titans.
When Jean discovers the body of his best friend, Marco during the clean-up operation in Trost. His vacant stare and the quiet way he pleads for someone to tell him what happened are heartbreaking enough, but the medical officer is correct when she tells him there's no time to mourn and she is relieved that at least this body can be identified.
Related to the above: Annie's whispered apologies to the mangled corpse of an unnamed soldier, during the same clean-up operation. She repeats it in shock, until Reiner speaks to her and reminds her that apologizing won't accomplish anything. All they can do is mourn and then move on. That they were the ones responsible doesn't make it any less heartbreaking, as it's clear just how horrified they are over the reality of their actions.
Episode 16, at least two of them. Which both involve Marco. Just as Jean is deciding which region he's joining at the Meaningful Funeral, he imagines seeing Marco, echoing his opinion that he'd make an excellent leader. As if that isn't heartbreaking enough, as soon as Jean declares his change of heart to join the Survey Corps, he bursts into tears. Major tearjerker there.
And when Eren finally learns Marco died, with nobody there to witness and tend to him as he was dying in pain. And on top of that, he sees Marco's spirit, too, this time wearing the special Scouting uniform, as if saying he'll always be by his friends' side.
The English dub makes both scenes just as heartbreaking as the Japanese version. Seriously, Mike Mc Farland really nailed Jean's declaration to join the Scout Regiment and his breakdown right afterward.
The beginning of Eren's return home after his first mission with the Survey Corps in the anime. At first the scene seems so light-hearted and triumphant, as he learns about how several of the members of the elite Levi Squadron actually pissed themselves on their first mission. Gunther gets everyone to finally calm down, but not without adding that he in fact did not piss himself. And then the traitor shows up and kills him...
And then in the next episode the rest of the squad engages the Female Titan. At first they seem to be on the winning hand, but then Eren remembers Levi's words, emphasized by Vogel im Käfig playing in the background. Before he can aid them, all of them are killed. And then Eren gets eaten... again... just as Mikasa arrives.
The scene in itself was heartbreaking. Anywhere from Eld dying before being able to realize what is going on, to Petra's incomprehension of the situation in her final moments and Oluo's horrified expression as he witnesses her die. The worst part of it all? Eren watches it all unfold in front of his very eyes, the very people who accepted him among their ranks and asked for his trust, gone, and he can only scream in horror. As the music grows louder, he completely loses it andfinally transforms into his Titan form once more.
And then we have Levi dashing through the trees, silently passing by the bodies/remains of his comrades. What makes the scene extra powerful is that his expression is deliberately obscured until he's found every one of them to be dead. The look on his face is absolutely heart-breaking. The whole scene is made even worse by the fact that a few chapters before, Levi explained to Eren that sacrificing a potentially large number of lives in the progress of combating Titans had become a normality for the Survey Corps, advising him to not let it affect him too much.
Episode 22 seems to exist solely to rip out the hearts of the audience, adding roughly half an episode of extra material just to rub salt into the wound.
The montage of the loved ones hearing the soldiers are returning, eager to see Eld, Oluo, and Gunther come home safely when none of them survived. The audience gets a slap to the face along the lines of "In-Universe they weren't just Badasses soldiers, they were people with hopes and dreams". Thank goodness everyone was spared the scene where some poor schmuck had to actually break it to them that their beloved fiancée/sibling/(grand)child didn't make it back.
Jean and Armin discussing their eventual deaths, while loading bodies onto carts. Connie and Sasha discussing dying, and whether it's right to celebrate being alive when others died.
Levi looking over the wrapped bodies of his squad.
When they're tossing the bodies of the cart, it focuses on Levi's reaction alone when he sees Petra's body flung out, Slow Motion style and with a heartbreaking score in the background. That, coupled with his initial reaction to finding her dead, and later having cut off a piece of her cloak to keep as a memory, only serves to imply that her feelings for him were returned. It just makes it even worse.
Dieter and his failed mission to reclaim the body of his fallen friend. This forces the abandoning of all the retrieved bodies in order to escape a horde of Titans. Levi having to declare his squad's bodies are "nothing special", and then watching Petra's body be tossed away. Later, he comforts Dieter by giving him a patch from a uniform, telling him it belonged to his friend. It was actually one he took from Petra's uniform.
When Eren wakes up, you can hear the despair in his voice. You can see he feels like a failure for letting the Female Titan get away and having Mikasa rescue him again.
Plus, the material from the corresponding chapter of the manga (the return of the Expedition).
Which is Eren coming back and seeing two children admiring the Survey Corps like he did. He breaks down crying.
Eren's great distress and denial over Annie being the Female Titan, where notably in the manga, he acts completely desperate for her to prove her innocence and Mikasa has to physically hold him back from running to her when the hidden Survey Corps members ambushes her. It goes to show how deeply he respected her and considered her a friend, serving as a contrast for later on when his great respect for Reiner vanishes instantly.
Annie is described by Word of God as a "normal girl forced to do horrible things", and her laughing in the anime when revealed as the result of all her "fear, shyness, loneliness and guilt" having a "relieved" outlet.
Annie's memories of her father resulting in Broken Tears when she's about to be captured. In the anime, there's the addition of Titan Eren snapping out of his rage when he sees her crying, and he's left staring at her in shock (and possibly pity).
Wall Sina, Goodbye gives some more insight on Annie's guilt. She internally grieves for causing many of her comrades' deaths after the battle of Trost - including Marco's - and, the day before the 57th expedition, goes to bed with tears in her eyes. What perhaps makes it sadder is that the entire day before the expedition, she helped solving a case regarding an abducted person and illegal drug sale, earning her heartfelt gratitude at the end despite her attempt at claiming she only did it for herself, serving to show her capability and will to help people when she's not ordered otherwise. At one point, she even reveals that she doesn't understand the reason for her mission and follows through with it solely because it's what her father ordered, which might make her both more sympathetic and more scary, considering how loyally she sticks to her mission despite not believing in it.
Connie discovering what remains of his village and the slow, horrible realization that something is very wrong. The way in which everyone desperately attempts to present him with false hope is heartbreaking enough, without the bonus implications that all the Titans they've encountered so far are/were his family and friends.
Reiner pitching himself out of a window to take out a Titan, even if he doesn't actually take the plunge. If he'd actually done it, he'd be forced to either reveal himself as the Armored Titan, or actually die in the fall. He's Becoming the Mask; given Ymir and Krista's conversation about choosing to die an unnecessary but heroic death so that you'll be remembered well, it's even more heartbreaking in retrospect. Despite being a Titan Shifter, some part of Reiner really does want to be true to the friends he's made among humans.
For that matter, his Villainous BSOD is difficult to watch. It becomes clear just how precarious his mental state has been for quite some time.
Chapter 43: Eren's rage at the traitors, Bertolt and Reiner. Additionally, makes the past scenes with the two harsher in hindsight...
In the same chapter, Mikasa had badly wounded Reiner and Bertolt, but wonders why she didn't go all the way by cutting their heads off. She then realizes she might have briefly regretted hurting her former friends when seeing their pained faces, which kept her from doing more.
Mikasa wakes up after the Colossal Titan fell on Eren only to find out everyone was knocked out by the attack and Reiner and Bertolt were able to kidnap Eren and Ymir, 5 hours ago. Mikasa breaks down how she never gets what she wants, to be with Eren.
Chapter 46 reveals that Reiner's guilt over his actions caused him to quite literally go insane, and flee into the false identity of a human Reiner to escape. He briefly lapses back into this persona, and is genuinely confused at Eren's hostile response to him. For bonus tears, we also learn that this whole time Bertolt has been helplessly watching his best friend go insane, and as a result they were unable to share any kind of emotional connection.
In Chapter 47, Ymir demanding to see Krista while on the verge of tears, because she's certain that it will be her last chance. And talking about how much it meant to her that Krista could smile for her, even knowing what kind of horrible person she really is.
Plus, Jean and Connie trying to talk Bertolt and Reiner down by reminding them of how they're all True Companions and promised to grow old together.
And on top of that, the mention that they knew Bertolt's sleeping patterns so well they joked about predicting the weather by them. There's no better proof that the Shifters' plan put both sides of their conflict in close, vulnerable proximity to each other.
Chapter 48: Ymir's tearful plea to Krista, and Bertolt finally breaking down when confronted by his former comrades.
Specifically, his cry of "Who do you think actually wants to kill people?" Remember that they were eleven when they attacked Wall Maria, and judging by their bond with the rest of the 104th, they're both genuinely decent people at heart. Not to mention the fact that they know that Titans are people. Whether they realize it or not, he was calling them hypocrites.
When Armin lies to Reiner and Bertolt about Annie being tortured, we see not only their worried reactions, but Eren's as well, implying that even after everything Annie did, he still cares about her to the extent he doesn't like the thought of her being tortured. While one could argue he was just shocked at Armin's lie, it's curios why his reaction is shown in the same context as Reiner and Bertolt's, and his expression overall looks more worried than simply shocked.
It's even worse that Erwin and his men are surrounded, Armin fends off a Titan with an injured Jean in his arms and Krista, Connie and Ymir continues kill much Titans as they can. Believing that this is the end of them, Mikasa thanks Eren for everything that he had done for her back then.
Ymir choosing to leave Krista behind, after everything she'd done for her. After Krista's declaration that they would live for themselves from here on, and swearing that she won't fear anything as long as they're together. After everything, Ymir gently caresses Historia's hair in Titan form and mumbles an apology to her, before running off to help Reiner and Bertolt. Historia's heartbroken expression as they ride off just makes it worst.
Chapter 51: Connie is... not happy about the fact that the Titan on his house is his mother.
The revival of the Levi squad has Eren remember the original squad and their deaths.
Levi processing the thought that every Titan he killed was an innocent human victim.
While the members of the 104th being made into a new elite squad for Levi IS pretty cool, when you stop and think about it for a second, you realize exactly how many Survey Corps soldiers have been slaughtered since the Battle of Trost and you realize that even the best of Humanity are only hanging on by a thread now if they've been pushed to using teenagers who have been part of them for less than a year as their elite unit.
Unless Levi was specifically recruiting Eren's friends in order to make Eren more comfortable, a sort of emotional crutch for Eren, which would move it into a heartwarming territory.
Chapter 50.5, a bonus epilogue included in Volume 12, is nothing but tearjerker moments. Having failed in their mission, Reiner and Bertolt are exhausted but try to get Ymir to escape so she at least will be safe. She refuses, expressing that she's grateful to them for saving her from her "eternal nightmare" and stating that she's the only one that can understand their circumstances. They're all people that weren't able to do anything with their own power, and she decides "playing goddess" (the selfless actions she used to criticize Krista for) isn't so bad. Reiner just looks plain exhausted, while Bertolt alternately apologizes to her and thanks her while crying.
In Chapter 55, as screams echo through the building everyone is in, Connie can be seen covering his ears with an expression like he's about to cry. Poor Connie really has been through a lot lately, and he's showing signs of hitting some kind of limit.
Erwin's past. He was curious like every child was and decided to tell his friends what he heard. And as a result his father was killed. You can just tell he blames himself.
In Chapter 56, Erwin demonstrates how he has to do the salute with his left arm now that his right one is gone.
Despite being shown to be a brat just moments before, the image of Reebs' son hiding behind a tree, having most likely witnessed his dad's murder, is pitiful.
In Chapter 57, Reebs' body is discovered and the Survey Corps are blamed for his death. Hearing people sneer at and condemn the Survey Corps when they're the ones who are trying to save them is beyond upsetting.
Jean, Connie, and Sasha are all still uncertain about taking human lives, Jean even doubting if he wanted to be apart of their plan anymore, as he admitted he joined the Survey Corps to help save humanity.
The deaths of the rest of Hanji's squad by the antipersonnel 3D maneuvering gear. Keep in mind that it's just modified 3D maneuvering gear, but the fact that this weapon, used by the Survey Corps to kill Titans so humanity can go beyond the Walls, is being used to kill humans in order to keep secrets at bay, is pretty disheartening.
Even worse, these people joined the Corps thinking that their death would come at the hands of a Titan, yet they are killed by the species they're fighting for and trying to protect, and with the aid of the gear they use no less. Dramatic irony at it's most tragic.
Levi's expression when he and Hanji's squadmates are attacked by the Humanity Suppression task force and the three squad members are killed via modified guns. First, it's startlement and confusion at what happened as Levi was barely able to avoid being shot twice, then you can see the realization setting in when he sees their bodies. This is someone who's a skilled fighter with swords and fists, and he's seen his own comrades ripped apart by Titans, but seeing them being killed with guns so swiftly, was something he was truly not prepared for.
The confirmation from Ymir that Titans do not eat for pleasure, but are instinctively trying to devour a Shifter in order to regain their human form. Hanji is also kind enough to remind us that these are most likely all innocent people who would never have done this otherwise, and have been trapped as Titans for who knows how long. As Hanji says, their existence is "another tragedy". Which is sobering considering it comes from Hanji, who has gone from hating the Titans as much as Eren, to becoming fascinated with them from a scientific standpoint to now feeling well-founded pity for them.
When Kaney Ackerman confronted Levi, in the bar in Chapter 58, he talked of how they both lived in garbage and how finding out about how vast their world had been a huge blow to Levi. It makes one wonder how he took it...
It's really hard not to feel bad for Jean; he entered the Survey Corps to help protect humanity and now he was deliberately being told to shoot to kill when the Human Suppression Task Force is on the Special Ops. trail. It gets even worse as he has one of the members at gunpoint, but he yells at her not to move or he'll shoot. His mercy ends up with him at the member's gunpoint after she kicks the rifle out of his hands and it leads to a Dead Hat Shot..
It's possibly made sadder that the one panically yelling his name is Mikasa. For all that she appears to barely notice his existence, we see that she does care about him and reacts frantically when it appears he's about to be killed.
The death of Levi's former friends and comrades in A Choice With No Regrets, Isabel and Farlan. What makes it a sad irony is that the events leading to their fate is very reminiscent of Eren's choice that inadvertently caused the death of Levi's squad later. In short, they're on an expedition when a terrible storm arrives, and Levi eventually makes the decision that he will go off alone to find Erwin and kill him in the confusion than stay with Isabel and Farlan. Shortly after doing so however, he finds the remnants of a Titan attack and realizes their footprints are headed straight back to where he left his friends. He internally scolds himself for making the wrong choice and arrives just in time to see Isabel getting eaten while she tearfully calls for her "Big Bro" (what she called Levi), followed by Farlan shortly afterwards simply waving his hand sadly at him before being devoured as well.
And it only gets worse from there. Levi proceeds to slice the Titan's belly open in a desperate attempt to save Farlan that way, only to pull out what's left of him. After a Roaring Rampage of Revenge towards all the Titans present, Levi comes across the severed head of his "little sister", a pained gaze still trapped in her eyes, causing him to fall to his knees in horror before stroking his hand over her eyes to close them.
Poor Armin after he killed the MP soldier who was about to kill Jean. He was seen in tears and throwing up outside of the squads' hideout and when Mikasa went to comfort him, he asked if she had felt like he did when she killed one of the human traffickers when she was nine. Then, even though he was feeling like shit, Armin immediately tried to apologize to Mikasa, knowing that he hit a sensitive topic with her and that he had gone too far, disregarding his own anguish and trauma.
What's even worse is that the whole reason Armin was able to take out that MP soldier was because she hesitated in shooting Jean. Armin lampshades this by remarking that that MP soldier was more moral than he was, as he didn't hesitate to shoot.
The MP soldiers' expression in the flashback in Jeans' perspective made it even more poignent. Until now, we've seen the Central MP like Kaney Ackerman and the rest of the anti-human task force as unhesitating in killing. To see a member of that same group hesitate to pull the trigger when the others before didn't reminds the viewers that even if they are enemies, you can't label them all as "evil".
Jean's guilt, justified or not, that his hesitancy forced Armin's hand is also rather sad.
Marlow and Hitch angrily denouncing the Survey Corps for the destruction of Stohess during Eren's battle against the Female Titan. They recount the great loss of life, once again hitting the reader with the fact that hundreds of people died in that attack.
Somewhat worse is Hitch's genuine sorrow for Annie. She has spent all this time believing that Annie was killed during the battle and that her corpse was too mangled to be recognized, and has only her roommate's possessions to remind her that she even existed. Her face when Levi explained that Annie was the Female Titan is just heartbreaking, and suggests that she really did think of Annie as a friend.
The entire injection scene as told through Grisha's eyes. We see the frightened, tearful Eren injected and when he transforms there is a panel of him screaming making it clear how painful it is. It only gets worse after Eren recovers from being a mindless Titan after he's eaten his father. At first there's just a look of confusion which slowly becomes absolute horror as he wails over Grisha's remains.
The fact that Eren who lost his mother to a Titan and vowed to kill them all in revenge became the very creature he hated and devoured his remaining parent.