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All the sad moments that have happened over the course of the story are listed below:
- When Ridley and Dark Samus attack Samus, they reveal they have revived and brainwashed Gandrayda, Ghor, and Rundas. Needless to say, Samus is beyond upset over this.
- Raven and Yang's reunion does not go well, with Yang coldly declaring that she didn't need Raven then and she doesn't need her now, resulting in Raven and Goro leaving in a beam of light with the Phazon Star. This bites Yang square in the butt in the third chapter when Ruby reveals how Raven's Semblance works and Raven has a bond for Yang and Ruby tells Yang that deep down Raven still loves Yang but Raven can't reciprocate that love if Yang pushes Raven away and that Ruby's not going to abandon her family because that's not what family does. Yang is in disbelief that Raven still has a bond with her.
- Dimentio forcing Ruby to see her Paper Counterpart’s descent into Chaos Ruby through memory flashbacks. This reduces her to tears and her family and friends went to comfort her after the stunt the jester pulls.
- Seeing Chaos Ruby hiding in a cave away from all her loved ones after the events of Super Paper RWBY and the death of her evil clone. Dimentio's actions continue to haunt her and she does not even realize that Dimentio is still alive and is going after her main universe self. Paper Yang and the others are searching for her, Yang is deeply hurt and concerned as to why Chaos Ruby ran away without warning.
- Falls under fridge somewhat, but when Pyhrra and Jaune arrive on Hat Kid's ship, she appears to be taking her friends exploring in space with her...and Mustache Girl is noticeably not present.
- Rosalina upon learning what Dark Samus did to the previous is reduced to tears and hurt by what she and the Space Pirates did. Hearing what has happened to her children, she doesn't know what to do.
- Gloria confirms to Marnie that the latter's in a bind, Marnie agrees and says if it was any other circumstance, she would do anything to stop them from defeating Bowser, but here she hesitates to try and stop Gloria from taking the Power Stars, even saying "just knock me out already", but Gloria eggs her on to have a fight. Said fight ends with Marnie pinning Gloria down and hesitating to finish her off but Gloria quietly tells her it's okay. Marnie hesitantly knocks her out and is reduced to tears as a result.
- Dark Samus stealing Megahammer from Bowser Junior, then cruelly taunts him over him wanting to use his creation himself. The kid runs off in tears.
- Poor Kokoro suffers a horrifying near-death experience in Haunty Halls Galaxy after she was nearly killed by the Phazon-infused monsters that were resurrected by the galaxy's Cosmic Clone-turned-Daredevil Comet no thanks to Dimentio. What's worse is that she even lost the will to speak in the following chapter given how traumatic this experience was for her.
- Chaos Ruby sees what is happening to her counterpart when she becomes Chaos Phazon Ruby, begging for it to stop. It is heartbreaking as Chaos Ruby is unable to prevent these visions from showing up or helping out her other self.
- Captain Slime while under the Phazon's influence revealed he carries a deep guilt over what his former friend-turned enemy Damian did to Marnie. This causes him to try and use Phazon in a misguided attempt to "cure" Marnie of the damage.
- While brainwashed, Mario reveals that he feels like the others have been abandoning him and once freed, reveals that wasn't from the brainwashing, but how he feels somewhat.
- Ridley's location for the final battle? K2L, just because he wants to mess with Samus by forcing her to battle him where they first met-her destroyed home.
- Becomes even worse at the end where, because Mother Brain set the planet to self-destruct, Samus and Chell have to watch their home be destroyed again.
- In the epilogue, Sheele confronts Seryu again and offers to help her get treatment. Seryu refuses, not because she doesn't want it, but because she thinks she's been broken for too long. Needless to say, Sheele breaks down crying and Ironwood is left wondering how Jacques managed to break her so badly.
