The story of KINGDOM HEARTS 0.2 Birth by Sleep ~A Fragmentary Passage~ is told in the form of flashbacks. Mickey, Riku, and Kairi are conversing with Master Yen Sid in his tower when Mickey mentions he once saw Aqua in the Realm of Darkness during his time there, and that there was more to the story that now needed to be brought to light.
The game then shifts perspectives to that of Aqua, who has been trapped in the Realm of Darkness since the events of KINGDOM HEARTS Birth by Sleep, and has been wandering for what feels like an eternity, trying to find a way out and back to the Realm of Light. In her travels, she comes across several familiar worlds that have fallen to darkness: the Castle of Dreams, Dwarf Woodlands, and Enchanted Dominion.
While exploring this section of the Dark World, Aqua is plagued with haunting memories of how she was unable to save her two closest friends, Terra and Ventus. As her travels progress, she becomes increasingly aware of the effect that spending so much time in the Realm of Darkness is having on her heart.
Eventually, Aqua’s path crosses with that of Mickey, who had managed to sneak into the Realm of Darkness through a portal just after an outside world had fallen into darkness. Mickey explains that it’s been 10 years since he last saw Aqua in the Realm of Light, and that currently, he’s looking for a Keyblade from the Dark World that can be used to seal the Door to Darkness from the inside.
He and Aqua team up and eventually reach another world Aqua had once visited: the Destiny Islands. It is here that the two of them find the Dark World’s Keyblade, as well as the Door to Darkness. Riku appears and works together with Mickey to close the door, while Sora, Donald, and Goofy attempt the same from the other side in the Realm of Light.
Meanwhile, Aqua tries to fend off a massive influx of Heartless threatening Riku and Mickey while they work to seal the Door. Aqua is thrown back into the Realm of Darkness in the process and once again, left without a means of escape.
Jumping back to present day, in Master Yen Sid’s tower, Mickey concludes his story. He and Riku set out with Yen Sid’s blessing to find a way to rescue Aqua from the Realm of Darkness, while Kairi is instructed to seek out Merlin, who is overseeing Keyblade training for both her and Lea.
Sora returns to Master Yen Sid’s tower alongside Donald and Goofy, and receives instructions to seek out an old friend who can help him regain the strength he had lost as a result of his recent clash with Xehanort in the events of KINGDOM HEARTS Dream Drop Distance. The three of them travel by Gummi Ship to the Olympus Coliseum, which remains to be explored in the upcoming KINGDOM HEARTS III!