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Tear Jerker: Sword Art Online
Volume Seven. All of it, both good (Asuna's reconciliation with her mother, Kirito's Big Damn HeroesYou Shall Not Pass, every damn heartwarming moment between Asuna and Yuuki)and heartbreaking.
Special mention has to go out to the end of the novel here, it is in this Troper's humble opinion the single most moving ending to any novel they have ever read Yuuki is finally succumbing to her lifelong battle against AIDS, and Asuna convinces the Doctor to let Yuuki log into the Medicube one last time before the end. They meet at the same spot where the originally met, and Yuuki gives Asuna Mother's Rosario, her one of a kind 11 hit combo. Following this the Sleeping Knights guild show up and pay their last respects, and Kirito & Co. do the same. Finally in one of the most heartwarming and breaking scenes in literature over 1000 players from the game put aside any conflicts and come to say goodbye to the Absolute Sword, who fades away after thanking Asuna for all she did and saying "I tried my best to live... Here, I really lived...". And to top it all off at her Real Life funeral over 200 players arrive in the flesh, surprising everyone at the hospital who thought she had no friends. Excuse me I need a moment...
Red-Nosed Reindeer, one of the sidestories. After Kirito joins the Black Cats of the Full Moon, they all get annihilated, including Sachi, a girl who reminds him of his sister, and someone he swore to protect. He goes through plenty of shit to find an ultra rare item that's supposed to resurrect dead players, and eventually gets it with the help of Cline and Furinkazan.... and learns it only works ten seconds after death. By that point, Sachi has been dead for six months.
Guess what story is the basis of episode 3 of the anime? You will never think of the song mentioned in the title the same way again.
Specially heartbreaking the moment when Sacchi actually hums the song while Kirito utterly breaks into Manly Tears. Bonus points for the darkly sad and lonely atmosphere of that inn room during Christmas Eve. You can argue the story is rushed for trying to fit everything in one single episode, but that specific moment totally knocked it out of the park.
Pina's death is heartbreaking, especially to pet owners.
Episode 22 has Lyfa guessing who Kirito really is. Lyfa/Suguha was preparing to forget her love for Kazuto by trying to love Kirito. She entered a brief Heroic BSOD when she finds out Kirito=Kazuto.
Kirito's first attempt to charge the barrier over the World Tree is heartbreaking. Even as he bounces off of it, he just repeatedly throws himself at it, showing just how desperate he is to reach the woman he loves. Not to mention the sight of Yui pounding her hands on the barrier, frantically calling out for her mother.
Leefa (struggling to stop him): Stop it Kirito, it's impossible! You can't get any higher from here-!
Kirito (cutting her off, nearly in tears):I have to!Damn it, I have to try!
His initial solo fight against the Guardians is both this and awesome. He's pushing with everything he has, more aggression than he showed even in his fight against Heathcliff, as memories of Asuna flash through his mind. With every one he sees, the more aggressive he gets. He wants to see his wife terribly and it shows.
Speaking of the episode, Suguha only tells him to leave her alone in the Japanese dub. If you look at the English dub...
Episode 12. That is all. Yui's reveal and Disney Death. She comes back in ALO but still...
Also serves for plenty of in-universe example. Just when Kirito and Asuna were starting to feel like a real family. Asuna crying in sadness only amplifies this.
Episode 13: Just as Kirito tells Asuna to stay back at the guild headquarters, she refuses, telling him she'd kill herself if Kirito were to die. After he admits that he'd rather run away with her just so they'd continue to live with each other, she reminds him that their real bodies don't have much time left. She then begins to cry in his arms, saying that she wants to live together with him in the real world.
In episode 14, Asuna dies in Kirito's arms after taking a strike meant for him. He picks up the fallen sword, surely ready to start a Roaring Rampage of Revenge...and swings weakly at his opponent. Just...no, strength, no speed, no technique. His opponent barely even has to dodge. He is clearly completely broken. then he's killed.
The second half of episode 15. Kirito learns that Sugou is planning to make Asuna his and tells the boy never to see her again. He is completely in tears in the subsequent scene, crying against Suguha's shoulders. Later we see Suguha lie beside him as he sleeps, shedding tears as well, but for a rather different reason.