Yume Nikki is a strange, unknown game, with no dialogue and a unique art style, so of course, the fans created many theories, some good, some bad, some complex, some that make us lulz. This article will categorize the theories by character. There will then by long theories with contributions from most characters, making a huge orgy of wild mass guessing.
NOTE: NOT EVERYBODY BELIEVES YUME NIKKI HAS A STORYLINE, AND MANY PEOPLE BELIEVE KIKIYAMA JUST MADE THIS GAME FOR THE LULZ. KEEP THIS IN MIND, THESE ARE ALL FAN THEORIES, AND THE ONLY KNOWN "OFFICIAL" STORYLINE IS WHAT WE CAN SEE IN THE GAME, LIKE MADOTSUKI'S NAME.
It's also worth noting that TV Trope's Wild Mass Guessing page on Yume Nikki contains a wealth of theories too, some of them more fleshed out versions of the theories seen here.
Madotsuki
Madostuki was raped.
In the game, there is much evidence that Mado was raped. In the Forest World, along a strange road, several creatures in the background with eyes watch over you. The last one's eyes follow you for a split second as you leave. Many claim these are ovaries, which adds "sexual content" to the game. Other incidents with eyes include the Eyeball World and the Barracks where entering a certain shed can lead to a tunnel where eyes follow the player. On the way to the Witch effect eyes in the trees follow the player. The theme of being watched seems prevalent.
Some say that Kyu-Kyu, a large colorful pole creature, rubbing the banister of a stairway, is phallic imagery. The Knife and Cat Effects alter the speed of which Kyu-Kyu rubs the rail of the staircase, speeding it up or down. Full-screen events feature an event called FACE, which is
achieved by going through a door right next to Kyu-Kyu. Some say it resembles a penis, fear itself, and/or static. The sequence in which the player stabs through a wall, leaving a bloodied hymeneal opening, leading to a seemingly benevolent phallic-shaped Kyukyu-kyun, leading to a terrifying FACE, suggests sexual assault to some players.
A dread of pregnancy (possibly originating from being raped) can be interpreted from monsters whose shape resembles a pregnant woman who has lost her head.
Madostuki lives in an apocalyptic world.
Madostuki seems like a perfectly normal girl, albeit possibly being a hikkikomori. Yet her dreams are strangely terrifying and eccentric, and she acts like she has been there before, displaying almost no emotion. That combined with the fact that her apartment is the only one in view, and she wont leave, and her TV doesn't get any channels, and her only source of entertainment is a NES game, it would seem that whatever is out there is worse than what is in her dreams.
Madostuki is a transgender.
She has a penis, and she doesn't like have a penis, so she cross-dresses, and wanted ovaries/vagina. It could be vice-versa. (See above)
Madotsuki is a lesbian.
Poniko is her image of a perfect beautiful girl she yearns connect with but can't because other girls she knew in the past weren't "weird" that way. She resorts to desperate measures to try and get Poniko's attention (going through different effects, flicking off the lights). Thing is, she feels her thoughts are dirty and she's afraid of other peoples' reaction. Uboa, a manifestation of that fear and guilt, pops up. The signs that people interpret as rape (Kyukyu-kyun + Face, the hands and eyes scattered everywhere, the decapitated pregnant belly things, etc) aren't signs of a past rape trauma but a dislike of penis, distaste of being watched by men, fear of judgment, and fear that she too will be expected to get married and give birth some day.
Poniko
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