One day, Sonoko, a married woman having a husband, meets young, beautiful Mitsuko. Puzzled Sonoko is charmed by the beauty of Mitsuko, and two people fall into relations between women at the start.

Set in Tokyo's otaku mecca Akihabara, "Akihabara@DEEP" tells the story of five otaku who drop out of society and end up founding their own successful IT venture called Crook. But Nakagomi, president of an influential electronics company called Digital Capital, will do anything to get his hands on Crook.

A mother is accused of murdering her daughter but when she tells her tale, things don't seem to make sense. Her husband says they have no daughter, there's a psychic that can trace phone calls, a blonde who sings the US anthem, a house with no bathroom, some Lynchian dream sequences, aliens, breeding experiments, very quirky FBI agents, and some other random events.

A paranormal researcher searches obsessively for a cursed home where something terrible happened to a mother and her child long ago.

In the middle of a riverside park stands a single bench. One evening, a couple of childhood friends who hadn’t seen each other in a while meet up at this bench. Although awkward at times, they sit there exchanging gentle words of affection.

When childhood friends Yui and Naoki are by chance reunited as adults, they begin to feel they were destined for each other. However, just as Naoki prepares to propose to Yui, he becomes embroiled in a mysterious incident and dies.

Now Naoki's soul wanders the world unable to express his true feelings for Yui. Yuzuru, a detective and the only person who can see Naoki, goes in pursuit of the truth behind Naoki’s death. At Naoki tries to use Yuzuru to talk to Yui, but will he be able to convey his message of love?

As children, the introverted Smile was being bullied by a gang of kids until the brash Peco comes by and chases all of them them away. Peco then takes Smile under his wings and teaches him how to play the game of ping pong. From there a life long best friend relationship comes into existence between these two polar opposite kids.

Five bizarre stories with no apparent connection to one another eventually become intertwined, resulting in surreal circumstances.