The game was originally planned to have alternate endings for Story mode for most of the cast except Double. There is unused text of these alternate endings complete with dialogue for what appear to be choices the player would make.

Filia: Would wish for her memories back despite Samson's protests

Cerebella: Asks the Skull Heart to make Vitale Mecidi love her and only her. When she returns home, however, Vitale has gone mad and murdered everyone present except Feng just so he can have Cerebella all to himself. Feng kills Vitale only for him to get back up, turned into a monster. Cerebella and Feng flee to the country, hoping to start a new life.

Peacock: She wastes time making inane wishes that the Skull Heart could not possibly grant, much to the Heart's annoyance.

Parasoul: Seemingly kills Umbrella to prevent another Skullgirl from being made. Umbrella reassures her with her dying breath that she did the right thing.

Ms. Fortune: Goes ahead with her original plan to revive the Fishbone Gang. They are revived as mindless servants of the now Skullgirl Fortune.

Painwheel: Wishes for "Freedom". The Skull Heart frees her from human emotion and restraint, making her into an incredibly powerful Skullgirl.

Valentine: Seals the Skull Heart away to prevent it being used again knowing that it can't be destroyed so easily. However, when she faked a deception against Brain Drain, she killed a character named Christmas, who was close to Brain Drain. For the sake of revenge, Brain Drain forces a control mechanism on Valentine and turns her into the same abomination as Painwheel. As this happens, the Skull Heart mocks Valentine's efforts.