- The entire plot of Haru and Tokaku's friendship.
- In the manga, Sumireko and Mahiru relationship is very sweet with Sumireko often acting as Mahiru's protector/Cool Big Sis like when Sumireko protects Mahiru from Takechi's bullying, or during the play Sumireko protects Mahiru from the stage light because as is later revealed Mahiru has an intense fear of bright lights, or the pool scene where Sumireko comforts Mahiru when after being blindfolded Mahiru starts freaking out.
- Also, Sumireko puts a flower on Banba's unconscious body as a sign of her expulsion but instead of leaving, Hanabusa actually stays with the unconscious Banba. She also asks Nio if it would be alright for her to take Banba back home so she can take care of her.
- The last chapter of the manga has Banba living with Hanabusa as a maid.
- Young Isuke being Happily Adopted by Eisuke. Yes, killing her abusive and neglecting parents wasn't pretty, and part of the deal includes grooming her into Eisuke's successor, but at least he adopts her, gives her a new name and life.
- Chitaru meeting Hitsugi for the first time.
- In the manga, Isuke and Haruki have a conversation about their motivations. Isuke reveals that her motivation is money and asks Haruki what could be more important. Haruki's Armor-Piercing Response was family. Isuke, of all people, actually stops and considers Haruki's answer before ultimately agreeing with her.
- The finale, where Everybody Lives. Haru successfully graduates from the Black Class and can live the normal life she always wanted with Tokaku at her side. Also, the other assassins seem to be better than before.
- Haruki still works for her family but has quited being an assassin.
- Hitsugi and Chitaru are still alive, but it seems that Chitaru hasn't fully forgiven Hitsugi for what she did.
- Sumireko decides to become more independent.
- Isuke is seen relaxing with her family in a resort and her "mother" consoles her for having failed to kill Haru.
- Mahiru is not dependable on Shinya anymore, but she seems to have changed for the better and has overcome her trauma of the light.
- Suzu visits her deceased boyfriend's grave for the last time, waves goodbye to him and proclaims that despite her eternal youth, she'll live her life to the fullest.
- Kouko decides to fight for her own freedom in honour of her mentor, and is seen gunning down two of her pursuers.
- The entire unaired 13th episode is the most lighthearted and heartwarming episode in the series. The episode takes place on a deserted island and the girls are playing another game. Only this time, the objective is not to kill Haru, but take the red medal she's wearing. The girls can use weapons that are located in chests across the island, but the weapons are mostly harmless toy weapons. In the end, the winner of the game is Ataru, who won by complete accident due to the medal landing on his head. At the end, Ataru and the girls hold a dinner where he expresses his wish to see all the girls graduate. It's truly endearing to see the girls getting along and not trying to kill one another. Even Otoya seems less murderous and has some downright adorable moments.
Heartwarming / Akuma no Riddle