- Painwheel's whole existence probably counts. Once just a normal girl, she was kidnapped and turned into a mind controlled, Anti-Skullgirl monster. Things go downhill from there. She seems to have regained control at the end of her story mode and attempts to go home, but her parents reject her and call her a monster. Not only that, but it is revealed that she is still without freedom, as the Skull Heart somehow took control of her, turning her into the new Skullgirl.
- The Dark Reprise of her Leitmotif, The Lives We Tried To Reclaim, playing in her ending does nothing to help with the sadness factor at all.
- Peacock's ending shows that she and Marie were once good friends. Marie reveals that she became the Skullgirl in order to rid the world of evil people like Peacock's slave traders and the Medici family. She does not wish to harm Peacock, who she calls Patricia, and asks her to go away, but Peacock decides to free her from the Skull Heart's misery. After listening to Marie's last words, Peacock decides to continue Marie's goal of destroying the Medici Family.
Peacock: Show's over friend.
- Before that, there's the destruction of the Anti-Skullgirls Lab. Peacock's on the verge of tears seeing how her friends and her father figure Dr. Avian was dying after Valentine wrecked the place.
- There's also her win quote after defeating Marie in her story mode. The fact that Peacock dumps all her insanity and wacky mannerisms and takes it completely seriously is both sad and unnerving.
- Squigly's story mode is already sad enough from beginning to end, but the post-credits scene of Filia standing at her grave drives it all home.
- "Here lie Sienna 'Squigly' Contiello & Leviathan. May they rest peace until we meet again".
- Has maybe the slightest tinge of Heartwarming, when you consider that Squigly will be coming back when the Skullheart reappears. Not "Goodbye", so much as "See You In A Few Years".
- In Valentine's ending, you can see Painwheel's absolutely lost look upon descending into the bowels of the chapel and discovering no Skullgirl but instead Valentine's discarded bonesaw.
- In Beowulf's story, it turns out that the Beowulf/Grendel title fight was rigged. The Canopian Kingdom commissioned the Medici mafia to drug Grendel before his fight to stack the odds in Beowulf's favor to make him seem like a great warrior and keep wartime morale up. Unfortunately, this had the side effect of Grendel dying in the fight, causing his mother to freak out and attack the audience, subsequently leading to her death when Beowulf had to take drastic measures. The Medicis basically forced Beowulf into unwittingly killing two people in cold blood, all in the name of patriotism. Especially heartbreaking when you take into account that Beowulf and Grendel actually had great mutual respect of each other outside of the ring.
- When Robo Fortune decides to deliver the Skull Heart but not before the Skull Heart asks how she knows if delivering it to Brain Drain won't result in a bigger tragedy. She simply states that she going to deliver it matter-of-factly, and without any of her usual zingers.
- While Parasoul's ending is saddening on it's own, the original plan was for the game to have Multiple Endings, and both of Parasoul's were bittersweet at best. Umbrella is on the verge of becoming the Skullgirl, giving Parasoul a Sadistic Choice between destroying the Skull Heart and catching her little sister in the blast or wishing on it to prevent her sister's transformation, at the cost of eventually becoming the Skullgirl herself. If you took the former, Umbrella dies in her sister's arms, while if you took the latter, Parasoul dooms herself to something even worse to save her life. Had the Multiple Endings system made it into the final game, players going through Parasoul's story would be greeted with a lose-lose situation.
- Perhaps the only character who would have gotten it worse than Parasoul was Painwheel; as already mentioned above, her life's already a living hell- and this isn't remedied in either of her endings. No matter which one them you would have chosen, Carol not only doesn't get her life back, but winds up becoming the Skullgirl. To elaborate, in her deleted ending, she wishes on the Skull Heart for her freedom- and is then "freed" of any and all humanity that she had left, becoming a Skullgirl of pure rage. In her canon ending, Painwheel destroys the Skull Heart and tries to return to her family, only for them to not recognize her and call her a monster. Brain Drain has her return, only to reveal that, even with the Skull Heart's destruction, Painwheel is bound to become a Skullgirl anyway- implied to be due to the Skullgirl-blood experiments conducted on her.
- While Cerebella may be base-breaking among fans because of it, there's no denying how disheartening her Story Mode's ending is. Having successfully lured Ms. Fortune to her with the Skull Heart, Cerebella sees that the only way to retrieve the Gem is to crush her to death. Blinded by loyalty to the Medicis to the point of setting aside her morals, if only for that moment, she goes through with it and returns the Gem as ordered. It's only when Vitale praises her for it that the reality of what she did hits home, and she can only look away shamefully.
- Just look at Marie's poster; it's full of stuff like 'Goodbye friends' and 'This is the end'. It is kind of sad to think that this is the last we'll see of Skullgirls, given Mike's and Alex's stated intent to move onto new projects, and also all the ideas that never got to see the light of day.
Tear Jerker / Skullgirls
Are you crying?! THERE'S NO CRYING IN FIGHTING GAMES!!
— Soviet Announcer