The story begins with Jennifer on a bus, asleep, with a little boy reading a storybook being the only other person on the bus. He wakes her up and asks her to read to him, but Jennifer is surprised to find that the pages are blank. The bus stops and the little boy runs away, so Jennifer runs after him.
The boy runs to an orphanage, where Jennifer sees two girls attacking something in a bag, and the boy entering the building. Jennifer finds a side gate, and goes to the attic, where the boy asks her to read to him again. The storybook now has words in it. Suddenly, there is an announcement that a funeral is about to begin. The boy advises Jennifer to go, as it is the funeral of one of her friends.
When Jennifer gets to the grave, it is empty, but some more girls push her in the coffin and carry her away. She awakens tied to a pole in an airship, and the boy (who she cannot see) tells her that she must find a gift for the Red Crayon Aristocrat Club every month, before cutting her free. She discovers that the first gift is a butterfly. She meets several people, who are all mean to her, except a girl named Wendy. She eventually meets a dog named Brown, whom she bonds with.
The two of them eventually find a butterfly, but the Aristocrats call it ugly, so they go and find another one. The Aristocrats still get angry, calling the butterfly worthless, and Amanda shoves a rat in her face, causing her to pass out. When she awakens, she finds a letter from Amanda, telling her to go to the airship's roof. There, Amanda apologizes for doing the torture.
The next gift is Wendy's missing pet rabbit, Peter. Jennifer and Brown find a bloody bag being beaten by Imps, who alert Mr. Hoffman, the orphanage director. Jennifer is forced to kill him, and the Imps drag his body away. Peter is inside the bag, still alive, so Jennifer takes him to the Aristocrats. They congratulate her, promote her, and demote Amanda. As a symbol of this, they let Jennifer perform the rat torture on Amanda, who passes out. Jennifer then notices that the rat is covered in maggots, and passes out as well.
Jennifer awakens in the same room as the boy, who gives her three storybooks to help her remember her sin. The next gift is Eleanor's missing bird, and Jennifer sees Diana and Meg talking about the bird. As they walk away, they drop a red feather, which Brown uses to find a trail of red feathers leading to a toilet stall. Diana and Meg come, so Jennifer and Brown hide inside the stall, listening to Diana and Meg mocking Eleanor.
Eavesdropping on Diana and Meg eventually turns out to be a bad idea, as they catch Jennifer. Meg explains the bird will die soon, and Diana and Meg have a bet on whether Eleanor will cry when she sees the corpse. Jennifer finds the bird, which Eleanor takes and donates to the gift box, in sadness. Diana and Meg follow her to mock her, leaving Jennifer alone.
Mr. Hoffman's fish is missing, so Jennifer realizes that it must be the next gift. However, she's wrong, as she finds Olivia crying over the gift box, which wants an "unmarried mermaid". She finds Meg and Eleanor, discussing mermaids, and they ask for Jennifer's opinion on whether or not they exist. Using a fish scale, Brown leads Jennifer to a fish-scented room, where they find Hoffman (now alive again), Clara and Diana searching for his fish.
Jennifer fights the Mermaid Princess monster, which leaves behind a mermaid doll. She takes it, but stumbles upon Hoffman, who is feeling up Diana. Diana takes the mermaid doll and gets angry with Jennifer. In the next chapter, Meg is missing something, and Diana and Eleanor reveal that it is a love letter to Diana. Diana explains that she already ripped it up, so Jennifer goes to look for the other half.
She ends up fighting the Goat Sisters, revealing the other half of the love letter inside the corpse of a goat. Diana, Meg and Eleanor enter, and accuse Jennifer off tearing up the letter, sentencing her to the "Onion Bag" note torture. During the torture, Jennifer passes out. Again.
By now, Jennifer has remembered her promise "Everlasting true love, I am yours". Having finished the storybooks the Prince gave her, she wakes up in the Aristocrats' club room. A pair of hands grab her and she passes out. The rest of the chapter is a flashback (not that you'd know just by playing). Jennifer awakens in a beautiful rose garden, with a farmer called Gregory Wilson standing over her. He mumbles something about his son Joshua and wanders off.
Jennifer follows Gregory, and ends up in his house, and has various memories of him, including him pointing a pistol to his head. In the basement, Jennifer finds Gregory, who locks her in Joshua's room. Wendy sneaks into the house and unlocks the door, taking Gregory's pistol as the two escape. The girls exchange Joshua's teddy bear for Wendy's brooch, with Wendy naming the bear Joshua.
Having finished her flashback, Jennifer wakes up outside the club room. The new gift is Joshua the bear, and the reward is a red crayon. Thus, whoever finds Joshua gets into the Aristocrats. Jennifer sees Gregory again, leaving a storybook outside Amanda's room. Amanda accuses Wendy of taking Joshua. Jennifer goes to see Wendy, who has fallen out of bed. She reveals that the Aristocrats came and accused her of taking Joshua.
Suspecting Amanda, Jennifer goes to find her, discovering that she is pulling what looks like a corpse of herself. Amanda goes to the top of the airship, but the power goes out and Diana orders Jennifer to fix it. After getting a stolen lever back from Xavier, Jennifer goes to the top of the airship, and sees Amanda beating something with a stick. Amanda gives Joshua back, and Jennifer sees that Amanda was beating a doll of herself, which causes her to faint again.
When she wakes up, the strange boy has taken Joshua, so Jennifer goes to look for it. Eventually, she finds it outside the club room, where she puts it in the box. She gets a crayon as she was promised, but lots of Imps appear and tie her up.
And this is where the story goes all David Lynch.
Jennifer wakes up tied to a pole, with red crayon marks on her dress... spewing red crayons. Hoffman says over the intercom that it is cleaning time, and Jennifer gets Brown to free her. In the hallways, Hoffman accuses Jennifer of trying to get out of her cleaning duties. All the other children are ignoring her when she goes to help, and people throw bits of paper with insulting messages on them at her. One note tells Jennifer to go to the main hallway, and when she does, day turns to night and Hoffman wishes everyone good night. Another piece of paper says that Jennifer is now the monthly gift.
Jennifer sees Wendy in the courtyard, but has to defeat several Imps before the door opens. In the courtyard, Wendy tells Jennifer that an important Aristocrat Club meeting is about to take place, and gives her a storybook. When Jennifer finishes reading it, she sees that Brown and Wendy are gone.
In the club room, Jennifer has a hallucination of Brown's corpse. All the Aristocrats appear, with Wendy revealing that she is the Princess of the Red Rose. Amanda whispers that Brown is dead, and points to a bloody bag. In a Crowning Moment Of Awesome, Jennifer slaps Wendy, calling her a liar and vowing never to forgive her. Jennifer then calls out the Aristocrats for listening to Wendy, and throws away Wendy's rose brooch. Wendy runs out of the room crying.
Jennifer wakes up in the night, and hears Amanda and Susan, who beckon her to follow them. She is shoved into the club room, where the Aristocrats ask her to be the new Princess. Jennifer accepts, and Susan notices Wendy outside, dressed as a boy. The others go outside to mock her, with Jennifer staying inside. Suddenly, Jennifer hears screaming outside.
The door to the orphanage opens and Wendy is standing there with Gregory, among the bodies of the children. Wendy has made Gregory into "Stray Dog", the bogeyman that Wendy used to scare all the children into following her. Jennifer defeats Gregory, and Wendy apologizes for being selfish. Stray Dog comes out and kills Wendy, who gives Jennifer the gun. However, rather than fight him, Jennifer gives him the gun, causing Gregory to come back into control and allowing him to finally kill himself.
In the last chapter, Jennifer is a little girl in the orphanage. She goes outside to see Wendy, and the two greet each other with kisses and curtsies. Jennifer goes out of the front gate and closes it, and Wendy lowers her head in sorrow. She remembers the airship crash which killed her parents, and finds Brown's collar in a nearby shed (she did the same at the beginning of the game). She makes the same promise to Brown: "everlasting, true love, I am yours." She promises to remember Wendy and Brown forever.
ExplanationOK, that left a lot of holes in the story. But with some other details, you can piece together the story.
Jennifer's parents and several other people died in an airship crash, of which she was the only survivor. She ended up on Gregory's farm, and as Gregory had just lost his son Joshua to an illness. Going insane, due to blaming himself for it, he dressed Jennifer up in boy's clothes, changed her name, and used her as a Replacement Goldfish. Soon after, she met Wendy, a girl from the orphanage. They began to exchange notes, and had a semi-romantic relationship. Their favourite game was "Prince and Princess", and Jennifer didn't mind being the Prince.
Eventually, Wendy saved Jennifer from Gregory and let her come to the orphanage. In the orphanage, Jennifer had a hard time fitting in, and, due to her chronic inability to stand up for herself, got pushed around by the other orphans, as well as the adults who worked there. Eventually, the adults disappeared for reasons unknown, and the children formed a cruel, despotic governing body called the "Aristocrat Club", which issued "Rules of Rose" that were akin to laws. Thus, the Orphanage became something like Lord of the Flies. At some point between Jennifer's arrival at the orphanage, and the disappearance of the adults, a number of orphans who never appear on-screen would go missing.
Wendy had risen to the top of the Club (unknown to Jennifer, and possibly all the other kids), having used the rumour of a Boogey-man figure named "Stray Dog" to scare the other children into following her, saying that the children who had vanished were kidnapped by Stray Dog. Rather than have Jennifer rule the club at her side, she used Jennifer's gift, a teddy bear (also named Joshua). To cope with how the children treat her, Jennifer made friends with a dog named Brown. This made Wendy, who had been described as chronically lonely before meeting Jennifer, violently jealous, and she formed a plan to get Jennifer to like her again (apparently unaware that Jennifer can love both a dog and a human at the same time). Her plan was thus:
1. Issue a Rule of Rose stating that Jennifer is to be killed, and her body given to the Aristocrat Club. 2. Change the Rule, stating that instead Brown must be killed. 3. Reveal herself as the leader of the Club, as thus the person who prevented Jennifer's death.
What Wendy didn't count on, was that Jennifer wouldn't see it that way, and would in fact, despise Wendy for what she had done. In a CMOA, Jennifer calls out not only Wendy for being a cruel despot, but every other person in the Club for following her. The Stray Dog legend was determined to be a lie, and the members of the Club decided that Jennifer was right, and she should lead them now. What they didn't know, was that Wendy had been using Gregory's insanity to control him by posing as his dead son Joshua (which also explains why Gregory, in his obsession, never came looking for Jennifer). She had been conditioning him (in one document, a witness describes it as "dog training gone horribly wrong") to kidnap, kill, and bury children from the orphanage, presumably, although not definitely, ones who had displeased Wendy in some way. Because Gregory was a farmer by trade, the disappearances were not connected with the freshly-dug soil on his property. Thus, Stray Dog was real.
When the Aristocrat Club overthrew Wendy, she brought Gregory to the orphanage and had him kill all the orphans besides herself and Jennifer. In a moment of horrible regret, Wendy apologized to Jennifer for what she had done, and handed her a gun Gregory owned, telling Jennifer to use it to stop him. Once she had done so, Gregory killed Wendy. Jennifer, instead of firing on Gregory as one might assume, gave the gun to him, and he turned it upon himself in a sudden moment of clarity. His final words were, "I'm sorry, Joshua."
It's unclear what became of Jennifer, but it is implied that she ended up surviving until adulthood.
It's also unclear as to what most of the game, with the airship and all that, really was, but there are some theories, chief among them, is that they happened more or less as they appear, save that they took place in the orphanage, and not on an airship, the imps and mermaid never existed, and Jennifer was the same age as the other children, since they had occurred in the past. This theory also holds that, the events of the game represent now-grown-up Jennifer reliving, and coming to terms with, her memories, with all of them appearing magical and twisted due to a combination of Jennifer being to young to understand everything at the time, and good-old-fashion Trauma-Induced Amnesia.