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Tear Jerker: X-Men
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Issue #41 of the Ultimate X-Men series is the second part of a series called "New Mutants". It breaks from the previous issue (which showed people in New York protesting against the Xavier School of Gifted Youngsters) by following a young teenager who wakes up one morning to find that no one is around. He goes downstairs, and his family is gone. He walks outside and there are people on his street, who spontaneously explode when he turns away. He goes to school, meets his friends, and then his friends vaporize in front of him. Frightened out of his mind, he runs into a cave. He is surprised to see Wolverine, who has been waiting for him. Logan gives the kid a can of beer, and explains to him over the last half of the issue that his mutant power has manifested itself when he hit puberty the night before: the ability to destroy organic matter. This is the final exchange of the book:
Boy: So, like...(sniffles)...like one chromosome or whatever to the left, and I woul'a maybe been one of the X-Men.
Logan: Finish your beer.
Boy: Just do it.
The final shot of the book is Logan leaving the cave. The expression on his face says it all.
Gambit being left in Antarctica by Rogue in nothing more than leggings. It was incredibly sad and cruel because if not for the events of his on-going series, Gambit's death would have been sure. They tried to explain it away later that Rogue absorbed his self-hate, but shouldn't she have hated herself then? It was just a maximum case of abandoness it breaks hearts.
Rogue: Home? Yo ain't got no home. Not with me, not with the X-Men.
Gambit: But... I love you...
Rogue: You're honest with the people you love, Remy. Otherwise... it's a gamble.
Later issues (between the abandonment and his return) stated that she did hate herself when it happened, and as soon as his personality faded from her head she spent every spare moment she could flying back to Antarctica to find him...Her failure to do so triggered another bout of self-loathing where she tried to get herself depowered through ''yet another'' phony mutant cure.
Ladies and gentlemen, as of recently in the X-Men, Kurt Wagner, also known as Nightcrawler, is dead.
It truly says something about him as a character that if you want to just hurt the X-Men, if you really want to snap them in half, literally, as a team you don't take out Cylcops, Wolverine, or even Charles Xavier himself, you kill the elf. You kill him and they will tear themselves apart.
Wolverine #147. When Archangel heals Abraham Kieros aka the first War and allows him to walk again. Specially with Abraham's words as Angel helps him get up from his bed, which were something like this (translating from the Spanish edition):
Abraham: Archangel...? I don't know how you did it. But I can finally start to move. I think I'll be able to walk! I don't know what have I done to deserve this, but thanks... Thanks for giving me hope again.
Cable's funeral in X-Men: Second Coming. Especially the shots of Hope giving his eulogy and telling everyone that he, as a soldier, got what he wanted out of life and that no one needs to shed tears for him — while she and Cable's father Cyclops are crying.
The bit where Cable died was even more wrenching. We see the techno-organic virus consuming him outside and in, and Hope forces her way over to stare in shock. She whimpers softly "Please...come back to me..." and right before the nightmarish spread of Cable blowing apart, he manages to look at her and give a tiny, hopeful smile. That smile, and the image of Hope laying down next to the only remaining part of his body, his metallic arm, and weeping, will haunt me to the end of my days.
The X-Men First Class story "Catalyst": Starting off with them all losing their powers (leading to a Tear Jerker for Angel when he wakes up to see his wings fall apart around him). At first they're attacked by a Sentinel, which prompts Scott to at first beg for his powers back, even though just a second ago he was cheering with joy at finally being able to see. But then later get them back, ten times stronger. However, since Xavier, Jean and Iceman are now godlike, Xavier decides that they need to give up their new found power levels. The others, Angel, Beast, and Cyclops are not godlike, Angel can now heal others and has bigger wings, Beast is now as strong as the Hulk, and Cyclops has gained control of his power. Upon hearing Xavier's reason for giving them up, which requires they all give them up, Scott is the first to agree with him, simply because he believes anything Xavier says. So Scott gives up the chance to have full control over his powers for once so his friends don't become drunk with power; while it's hard to see, it looks like he's about to cry from the sacrifice.
The scene in the X-Men crossover Necrosha in which Warlock rescues Doug from the techno-organic zombies, by summoning a pair of sentient guided missiles he had created.
Missile 1: "Self/Father has need of our help?"
Missile 2: "Is it time to create the final boom?"
Warlock: "With sadness, affirmative.
Missile 1: "Sadness is not appropriate input, Self/Father."
Missile 2: "Was it not for this purpose that we were made?"
Wolverine's son Daken meets a beautiful, sociopath FBI agent and tries to make her "realize" that she loves him. She does not, or is unable to, feel the same about him. In fact, she thinks he's no better than the criminals she puts away everyday. Seeing Daken realize that he can't make this one, normal woman love him, that he can't have this one good thing in what's been a pretty miserable life, is pretty painful...especially if it sometimes feels as if I'm going through the same thing...
The first issue after M-Day of New X-Men, when hundreds of young mutants woke up powerless. Not because it was epic or melodramatic, but because it was a very realistic portrayal of the confused mindset of teenagers. Without their mutant abilities and features, friends couldn't recognize each other and some were scared of one another. A couple kids refused to believe their powers were gone and died trying to use them again. One kid was punching a wall as his fists were bleeding, happy to be able to feel again. It was a painful analogy of the horrible crap that happens to teens in the real world.
The last issue of M-Day. All of the heroes are fighting one another, and someone comes to the realization that it's Pietro that had caused this reality to exist in the first place because he wanted to save Wanda. The last moment before everything flashes back again always gets me, especially with the lone tear running down Wanda's face. "Daddy, no more mutants."
And the earlier scene, where Pietro is demanding that their father do something because otherwise Wanda will die, and Erik just looks so tired and helpless and can do nothing but turn away. Magneto, MASTER OF MAGNETISM, being absolutely beaten by the world is a Tearjerker on its own, and then you add in Pietro's literal collapse, and Wanda's quiet exhaustion— She's been pulled out of her bright, happy world so many times since we've last seen her, she actually accepts that her friends will come to murder her as a relief.
Joss Whedon hates his characters. Even his favorite ones. That is the only way to explain the end of his run on Astonishing X-Men, where Kitty doesn't die... she is just forced to drift intangibly through space, probably forever. Don't bother hating him for it, he probably hates himself too.
Jean Grey's death at the end of the Dark Phoenix Saga, particularly after Uatu's poignant statement at the end: "Jean Grey could have lived to become a God. But it was more important that she die... a human."
Colossus' sacrificing himself to release the Legacy Virus cure. Even though you knew they'd get around to bringing him back eventually, it was a touching scene.
Illyana's death in the '90s. Especially UXM #303, which focuses on Jubilee's reaction to the death.
Psylocke's death in Xtreme X-Men. After gravely wounding Beast and Rogue, Vargas steps up to battle against Psylocke. We see her raise her psychic katana, and then we are shown a close up of Beast's eyes. Three panels of this later Psylocke is being held in his arms, fatally stabbed in the abdomen as Rogue sobs in Storm's arms. Her funeral next issue was also a tear jerker, outside watching the airplane that is to carry Betsy's ashes back to England, we get a look at the faces of Storm, Bishop, Beast, Neal Sharra, Rogue, and Sage. Each one of their expressions says it all. Then we see a visage of Betsy in the clouds, her arms raised upwards as she smiles.
Granted, she returned a few years later, but it was still depressing to see her die, even finding out Claremont didn't intend for her to die.
In an old issue of New Mutants, Danielle Moonstar uses her Valkyrie powers to stand between Death and a childhood friend who was in a car accident...until Death tells her that her friend has slipped into an irreversible coma; Danielle can keep him from dying, but he will never wake up. Grieving, Danielle stands aside, and from inside the hospital room we hear the monitor flatline...
A surprising one for Sabertooth of all people. In one of the Wolverine mini-series, Wolverine and Sabertooth (Pre-Heel run) are running the first school for mutants and early on they find a woman with the ability to make illusions so real that your mind makes them so. Even if you understand they're just illusions. In the end when the feds are attacking Sabertooth and the woman Holo run off together on a motorcycle and make a new life for each other, getting married in Vegas, having kids, growing old and her death of old age. A happy end to a happy life. Except that it's all an illusion on her part to give Sabertooth some kind of happy memories to give him a sanctuary from his miserable life and dies. It destroys him and turns him into Logan's enemy since the class was all his idea. Tears don't begin to cover it.
X-Men Legacy #300. An unnamed girl left horrifically scarred after fighting off an attempted rape by a popular football player that caused her town to turn against her (in a clear parallel to a number of similar high profile incidents) tries to sneak into the Jean Grey School thinking that, as a deformed freak, the X-Men are the only place she'll fit in. However she's caught in the security system and slowly sucked in to her eventual death when an older man walks by, introduces himself as Forget Me Not, and tells her his story. He's been a member of the X-Men for years but due to his powers, people instantly forget him when they look away, nobody remembers leading to a lonely existence but one he finds fulfilling helping the X-Men from the shadows. Eventually he switches himself for the girl in the security system and tells her to go out and live. And of course as she turns away she instantly forgets him and ForgetMeNot's fate is left ambiguous.
Girl: But it's not fair! People should know! People should know who you are and wh... what you've done a—
Forget Me Not: C'mon, miss. Weren't you listening? The way the world sees you isn't nearly as important as the way you see it. And the things you do to make it better. Big or small, kid, it all adds up. A legacy's worth more than the person who leaves it. You're beautiful. Go do something incredible.
Rachel Grey's entire damn life. Her mother died when she was a little girl, which would be bad enough, but then the government builds the Sentinels to hunt down mutants. The Xavier Institute is laid siege to by soldiers, and she witnesses Professor X getting shot to death. Then she spends most of her childhood being horribly experimented on and turned into a weapon designed to hunt down and capture or kill the last of her kind. Once they run out of Mutants, the government throws her into an internment camp with what's left of her friends and family. In a last-ditch attempt to prevent this timeline from existing the remainder of the X-Men assault the Sentinel stronghold, leaving only Rachel and Katherine Pryde alive. During this, Rachel feels her boyfriend's death, along with what he was feeling as it happened. And just to make things worse, while Katherine survives, their timeline doesn't change. So Katherine makes a deal with the Phoenix Force to send Rachel into the past, in the hope of giving her a better life. To the X-Men, in the nineteen eighties. Things got worse before they got better. Then they got worse again.
Cypher's death in New Mutants #60. Doug takes a bullet for Wolfsbane, and she doesn't even notice. The next few issues focus on the New Mutants grieving. As a bonus, #61 has them learn about the X-Men "dying" in Fall Of The Mutants, so we also get Illyana's grief over her brother's death.
The 2011 anime kicks off with it's own version of Jean Grey's death before the opening credits even start rolling. She goes all Dark Phoenix due to Mastermind's mental tampering, and suffers a super powered meltdown.
When Emma allows Xavier to see her memories, we see the reason she left the Inner Circle. After she once used her powers to manipulate a wealthy man into giving her his entire fortune, he committed suicide shortly after. That and her being shunned by everyone for most of her life, especially bad for her since she knew what they were all really thinking of her thanks to her powers. With the way people treated her, it's no wonder she started using her powers to get back at the people who ostracized her.
Poor Takeo'sentire backstory, never got the chance to know his own father, super powerful (and dangerous) mutant powers manifest at a young age, forced to erase the memories of himself from all his school friends before being hidden away from the world by his mother. The kid never had it easy.
Which accumulates into his eventual death by Super Power Meltdown. Which by the way happened when he was about sixteen.
Kōichi and Riko, murdered by the Inner Circle, and just after they'd been cured of the virus no less.
The 90's series
Anything related to Morph. Specially the episode dealing with his PTSD.
Also, anything related to Proteus. Yeah, his backstory and powers were all bowdlerized, but it's still damn powerful stuff.
The series's rendition of the Phoenix Saga. Where do we start?