What's even worse is what's finally confirmed in that very episode; the whole reason Asuka is Jerk Ass and the whole reason she uses "doll" like it's an epithet on par with the n-word is because part of her mother Kyouko's soul was sucked into Unit-02, leaving poor Kyouko clinically insane and incapable of loving her own daughter, treating a little rag doll like the actual Asuka. Kyouko then hangs herself on the very day that Asuka is chosen to be the pilot of the very robot that, without her knowing, drove her mother insane; she enters the hospital room while happily babbling about how she will save the world in the EVA 02, only to find that Kyouko has hung herself.
In the manga, they actually made it even worse: just before committing suicide, Kyouko attempts to murder Asuka by strangling her. This eventually causes Asuka to attempt the very same thing on Shinji, in lieu of the infamous Dude, She's Like, in a Coma! scene.
The anime also has shots of said rag doll hanging from its own little noose — recall that Kyouko thought this rag doll was Asuka. Oh, and don't forget the voiceovers of Kyouko asking Asuka to die with her and Asuka desperately agreeing and pleading "Don't stop being my mama..."
Young Asuka crying Berserker Tears screams at her mother (supposedly) "Why won't you look at me?!"
Any time Shinji screams.
Most of episodes 16 to 26 have some element of this, due to being the show's descent into insanity.
The end of episode 18, where Shinji is powerless to stop Gendo from murdering unit 03.
For a little recap on what happened: when Shinji realizes that someone is piloting Unit 03, he staunchly refuses to fight even as Unit 03 pins him to a mountain by the neck because he would rather die than kill another human being. Gendo then tells the staff to switch to the dummy plug, and the control locks down over Shinji's hands as the plug takes over. Then Shinji is forced to watch (and possibly feel) Unit 01 completely brutalize Unit 03 (tearing off limbs, ripping out intestines brutal) as we pan to a shot of Gendo looking at his son impassively and the NERV staff listening in horror all the while Shinji desperately screams for Unit 01 to stop.
The manga version of the above episode is even worse for a lot of people, as Shinji actually ends up killing Toji.
Nearly anything with poor Shinji that isn't a relentless Narm.
That image of a little Shinji crying with bags full of his clothes around him. His dad just disowned him and left him with his aunt and uncle while Shinji begs him not to go. Just... he really needs a hug and his father needs a brutal No-Holds-Barred Beatdown and a "Reason You Suck" Speech.
Episode 24. After 23 episodes of relentless mental torture, Shinji finally finds someone who understands and loves him, and he turns out to be the final angel and Shinji has to crush him with Unit 01's armoured hand. Even worse when you realise that since the Eva-s and pilot are synched, it will feel like Shinji has killed him with his bare hands. God, it sucks to be Shinji!
Kaworu was the first one to say that he ever loved Shinji. In all his fourteen years of living, Shinji has never once, not from a friend or a guardian, heard somebody say 'I love you' to him. Somebody just needs to give the poor boy a hug.
Speaking of Episode 24, we start off with a flashback of Asuka finding her mother's body hanging from the ceiling of her room with the doll that she thought was Asuka. As if watching her reaction to that wasn't tear rending enough we flash to the present to see her in a crumbled apartment bathtub with sunken in cheeks sitting in vaguely blood colored water implying she had tried to slit her wrists while mumbling about how useless and pointless her life was.
The end of episode 21 deserves a mention, too - namely, Misato breaking down while listening to the last phone message Kaji left before his death.
It's worth mentioning that his actual death scene counts as his Crowning Moment of Awesome as he casually asks his assassin, "What took you so long?"
Ritsuko's mother strangling little Rei to death. She then realizes what she'd done and commits suicide.
Misato bidding farewell to Pen-Pen was not exactly a Tear Jerker, but it was sad to see the resident comic relief penguin go. And then, depending on which finale (original 25-26 or End) you believe is the true ending, things either got worse or near-infinitely worse.
There's also both of Rei's heroic sacrifices. The first time she almost died protecting Shinji, but he managed to save her. The second time it happened in reverse - he ran in to save her, but she died protecting him.
This particular scene was awful since Thanatos was playing in the background. To top it all off this is one of the few times we see Rei express emotions in the anime, even crying.
It's even worse in the manga. When Rei sees Shinji coming to rescue her, the Angel (which is bonded with her at the time), rushes towards Unit-01, taking the form of lots of Reis who all lovingly embrace the Eva. Rei notes that this is her heart, which wants to "be with Ikari" - and Shinji has to cut all these Reis off with his prog knife. He tries and utterly fails. So she reverses the AT Field, containing the Angel in Unit-00, and blows herself up. And they give her a Really Dead Montage when Shinji remembers all the special moments they had later that night, whilst sobbing his heart out.Wow.
And of course, Ritsuko's complete mental breakdown. Specially when she recalls Naoko's mistake of falling for Gendo, and calls herself stupid and worthless because she committed the same mistake 10 years later.
Touji. Hikari. That. Is. All.
To extrapolate on this, Touji was one of the few "normal" characters in the show. No underlying emotional trauma, good friends, relatively normal life all around. Then Shinji accidentally injures his sister during one of his battles with the Angels, and he is subsequently selected to pilot Unit 03. What does he get for his trouble? Being horrendously mangled by a dummy plug controlled Unit 01 beating the hell out of his Eva and then CRUSHING HIS ENTRY PLUG, which leaves him confined to hospital bed and with an AMPUTATED LEG! Not only does his life go horrendously to hell just by mere association with Shinji, but him lying broken and battered in a hospital bed is the last we EVER see of him in the series. Either he had to go through life altering amounts of physical and psychological therapy, or he got to experience the hell of End of Evangelion personally, depending on which ending you take as the true ending.
Something all of the episodes have in common, but only really sinks in around episode 18: heart-breaking, traumatizing action, horrendous tragedy, episode ends, and... "Fly me to the moon, and let me play among the stars..." That song becomes so disturbing.
The fact that, in Evangelion, both Adam and Lilith fell on Earth traveling in "moons" (Adam brought life on Earth, and Lilith initiated the First Impact which ultimately resulted in mankind) makes it way more symbolic. "Flying to the moon" basically means returning to the Black Moon (Lilith's moon), thus merging into a single being. This song is an huge foreshadowing, starting at the very first episode.
Asuka sobbing over how she hates herself at the beginning of episode 22.
Misato saying in Episode 25 that she hates herself and doesn't know how anyone could love her.
End of Evangelion
Ritsuko deserves a mention here. She installs a firewall to keep out the hackers for a couple of days, but while she is doing this she tries to sabotage Gendo by changing plans. It doesn't work. The computer she was working with was based on three sides of her mother, Naoko's, personality Melchoir-1 as a scientist, Balthasar-2 as a mother, and Casper-3 as a woman. Her mother? She was Gendo's mistress. Just like Ritsuko.
Ritsuko: A loving daughter's final request - mother, let's end it together. (pushes a button on her PDA but nothing happens) It's not working? Why?! (red NEGATIVE blinking next to Casper) Casper betrayed me? Mother, how could you choose your lover over me?!
If you know it's coming, Misato's death scene is especially gut-wrenching. Especially hard-hitting is the speech she makes beforehand. She knows she's dying, and she spends her last moments trying honestly to help Shinji and bring him out of his BSOD, even using her own death to try and shock him back into action; trying to show that even if it hurts and everything seems to have gone to hell (which by that point, it pretty much has), you can still step forward.
Misato: "That's an adult kiss, we'll continue the rest when you get back"
Shinji sobbing silently in the elevator while clutching the handkerchief with Misato's blood on it.
Shinji rejecting humanity due to him suffering from rejection too much in End, resulting in everyone on Earth to melt into LCL and die (especially with Komm SŘ▀er Tod playing. The title is German and means "Come, sweet death".).
Also consider this: the event took place at midnight, on New Year's Eve, 2015. Humanity didn't see 2016 besides Shinji and maybe Asuka.
Gendo's part in this scene. He finally realizes that he wasn't a good father to Shinji, only to be killed. Everyone in the world is confronted by the one person they want most, so that they let down all the mental and emotional shields that separate them from each other. The thing Gendo wants most in all the world? To be violently murdered by his son. GOD.
You can also see that scene as Yui taking her revenge on Gendou for abandoning Shinji, and thusly cutting him out of his greatest dream, Instrumentality, entirely.
Asuka's death is pretty hard too. It's especially crushing because she had just crawled out of her Heroic BSOD and seemingly destroyed her enemies in one of the greatest mecha battles ever. She fails entirely because of circumstances that she couldn't affect. And the act itself was sickeningly brutal: Eva-02 is mutilated, torn apart and devoured, and Asuka with it because of her synch-ratio.
Shinji: Nobody cares whether I exist or not. Nothing will change. So, everybody just die.
Rei: Then, what is that heart for?
Shinji: It'd be better if I wasn't here either. So I should just die, too.
Rei: Then, why are you here?
Shinji: Is it okay for me to be here?
Young Shinji building a sand castle on his own, then crying and kicking it down.
The moment just before Shinji begins Instrumentality. He's curled up in the EVA cockpit, falling to pieces, screaming, and then he looks up and sees Kaworu, smiling, and for just a second he looks so overwhelmingly happy, for the first time in God knows how long. It's just heartbreaking to realize that Shinji is so broken that a single smile from a boy that he only knew for a few days means so much to him.
Like much of End, the very last scene is both disturbing and heartbreaking: Shinji trying to strangle Asuka with a blank face, and then he just breaks down crying.
What Asuka does deserves clarification: reach out and touch Shinji's cheek. Keep in mind that she's severely bandaged up/ still wounded from her fight with the Mass-Produced Evas, possibly took all of her mental willpower to come back out of the LCL and reform her physical being, AND is being choked while in this vulnerable state. Then, thinking back to Shinji's internal struggle (where Asuka called him "worthless", hence why he's choking her) up to this point where Shinji realizes from this one, affectionate gesture that he's wanted and has worth to someone...
Pen-Pen is usually the Plucky Comic Relief in the series. However, his appearance in the movie where he watches Shinji confront and strangle Asuka, seeming very confused, just somehow seems to hammer in how depressing it gets.
During the famous LCL transformation scene all of the characters featured meet their loved ones and are at a moment of happiness and peace before they die/reborn, except for Shigeru Aoba, who hides under a table terrified at the army of Reis, showing that throughout his life he never found a single person he ever loved.
After Unit 01 rips apart Unit 03, the rescue team reaches the entry plug and finds that Toji is dead. We then see Hikari smiling and planning the lunch she's going to make for Toji. This is one scene where the manga manages to be even more emotionally wrenching than the anime. "This time he'll like my lunch for sure... I can't wait to see his face..."
And then after Hikari spots Shinji outside of school he runs away. Kensuke suggests going after him but Hikari says that it's probably for the best because it will never really be the same between them anymore. She isn't stating it in anger but as a sad fact that can't be changed.
Kaji's backstory in the manga. He was orphaned by the Second Impact and put into an orphanage, which he escaped with five other kids, one being his little brother, to go around stealing things to survive. They found a military base and began robbing it for food, until one day, Kaji was caught. He was beaten by a soldier and asked where his friends were. When he didn't say anything, the soldier threatened to use deadly force on him, pointing a pistol with a trigger pull of two-and-a-half kilos at his head. Kaji was so scared of death he told where his friends were. The soldiers went to find them, he knocked out one of the soldiers guarding him, and ran. When he finally found his hideout, the soldiers were already leaving. He peeked inside... every one of his friends had been summarily executed, including his brother. They died so that he may live. The saddest part is, this is probably what would really happen in a post-apocalyptic situation such as this. It's enough to make some of the most hardened of us well up.
Although he doesn't show it, it's revealed in an artbook (and in the manga version) that Kaji is a self-hating mess. In the manga, he describes himself as "someone who does not deserve to be happy" (which is the reason for his extremely dysfunctional relationship with Misato).
While Kaworu was definitely more of a villain here than he was in the TV series, his death is actually pretty tragic, probably more so here than in the show, primarily in how it's setup. While in the anime it's set up as a self-sacrificial moment, in the manga it's very clear that Kaworu just wants Shinji to Mercy Kill him, since SEELE will do it anyway if he doesn't initiate Third Impact, which is, of course, his only other option. Shinji doesn't want to do it because he doesn't want to lose anybody else, even though he continually made it clear that he didn't like Kaworu, but he complies. And instead of showing Kaworu's head falling into the LCL pool, we are treated to Shinji's perception of how he views the scene, which involves him personally strangling Kaworu to death in the very place they first met.
Gendo is an irredeemable asshole in the manga - power-hungry and ruthless, and a world-class nihilist to boot. The assumption that, like in the anime and EoE he might feel remorse for the way he treated Shinji, despite his reasons is shattered when, upon the anniversary of Yui's death, he notices Shinji wanting to reach out to him and shoots him down saying: "Don't try to think that we can understand each other. For some reason, people think they can do that. Remember that they can't. Never completely, never enough."
It gets sadder toward the end: Gendo DOES end up feeling remorse for how he treated Shinji... as he's dying. And as he dies, he remembers that when Shinji was just a baby, he DID feel love for his son, but was too scared of the notion of being a father to become close to him. He regrets this deeply, and his last thoughts are hoping that Shinji survives and lives a better life.
In the anime, Gendo dropped Shinji off at a train station for him to be taken in by Shinji's "sensei" (a teacher or possibly a caretaker whose name and gender are never mentioned even once). However, in the manga, Gendo drops Shinji off to live with his uncle and aunt. When confronted by Misato at the train station, Shinji says, in tears, that he "doesn't want to go back to where he was." We are shown in a later chapter that one, he didn't live in the house itself, as his uncle and aunt saw fit to make him a room in the backyard shed, where he stayed, contributing to his feelings of abandonment. Second, there is an incident where Shinji finds a bike lying in the trash, picks it up, and a nearby police officer takes him in for theft. Gendo doesn't come like Shinji was desperately hoping him to, and when his aunt and uncle come, they scold him for stealing the bike and don't believe him when he pleads with them that he didn't steal it.
In the manga after Asuka speaks to her stepmother on the phone, she runs to her room and throws herself on her bed. She stares into the dark for a while, then says 'mommy', with the most heartbreaking expression on her face. It just really hits it home that for all her bluster Asuka is still just a kid who wants to be loved and comforted. Even though her mother died ten years ago, Asuka still desperately looks to her for guidance.