Mio is in her second year of high school, and is a girl who just sort of gets by. She doesn't really do homework and she's not good at making a real effort at anything.
With her childhood friends Arata and Madoka, she often goes to hang out in Ikebukuro after school and they generally have a good time. Until Madoka tells Mio that she's starting to have feelings for Arata; this immediately makes her realize that she too has feelings for him, but not wanting to ruin their relationship, she tells Madoka she will support her.

Mio is confused and starts avoiding Arata, keeping him at a distance, which eventually leads to them fighting. This makes Mio realize she's been running from her own feelings this whole time, so in order to make things right she decides to talk things through with Arata. However, on that rainy day, as she is on her way to meet him she ends up in a traffic accident.

When Mio wakes up, the world is completely different. Around her trains run on water with beautiful whales swimming next to them...

She's in a place she's never seen before.

When she goes to the station and exits through the ticket gates, she's in Ikebukuro, a place she knows well! But it's still slightly strange..

She continues walking through the streets until she meets Gimon, a character who claims to be "the guide in this world". Gimon tells Mio that she's currently in a reflection of the world, and there are doors that lead to the world Mio wants, but...

"You shouldn't listen to Gimon anymore, let's go back!"

Out of nowhere a mysterious girl, Kiku-chan, appears and stops Mio from opening the door. She tells Mio that the proper way to get back to the real world is to go to Lost & Found. Once there, Mio learns that she needs to find a lost memory from her world and convey how strong her desire is to return. Mio tries to find a way back home with Gimon and Kiku-chan, but for some reason she can't recall the lost memory she needs. And since she can't answer, the staff disappears...

"I miss Arata. I need to tell him something!"

There's just one way for Mio to return to Arata... she needs to walk around in an empty Ikebukuro to find that precious, lost memory among all the other memories she has in this part of town...