The dormant powers of Kuwabara have awaken, as he continues his fight against Seaman. Seaman realizes that Kuwabara is the one that can shatter barriers between different dimensions. Using his new spirit sword, Kuwabara frees his friends and defeats Seaman. Kuwabara brings his friends, along with Seaman, back to his home. Seaman talks about a video called Chapter Black, showing footage of victims of humankind's atrocities against their fellow men. Viewing of this footage can change a human against its own kind. Shinobu "Black Angel" Sensui, is revealed to be a former spirit detective, unveiled as the mastermind behind the plot to remove the barrier to the Demon World.

The story begins in the Spirit World, where the River Styx is overflowing, due to a tsunami. But as Koenma looks out his window he can tell this is no ordinary storm. The floodwaters continue to rise, and just before they become too much for Koenma he gives a mysterious item to Botan, and tells her to give it to Yusuke Urameshi. But Botan gets hurt badly and barely makes it to Yusuke. Botan is too weak to give Yusuke the item. Throughout most of the movie she’s unconscious and is unable to do anything, while a great evil is surfacing. The storm was apparently caused by the forces of the Netherworld, which was banished into cold space ages ago. All this happens pretty quickly, and so does the fighting. We get to see Yusuke and the others do their signature attacks, against some of their toughest opponents yet. To restore balance in the now flooded Spirit world, Yusuke and the others must track down five spots on Earth that contain a large amount of spiritual energy. But their simple plans get turned upside down when the ruler of the Netherworld, Yakumo, and his three henchmen decide to use the same energy for evil. So, the race begins to save the Spirit World, and now the Human World as well.

Kaitou's devious game becomes a fight for survival as Hiei, Botan, and Kuwabara all fail prey to the twisted teen's bizarre rules. But Kurama issues a challenge...one by one the letters of the alphabet will become taboo. If any of the taboo sounds are uttered, the speaker will face a terrible penalty. Placing his own soul on the line, Kurama prepares himself to battle wits with the brilliant Kaitou.