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The Winds of Water is the name of a deadly storm that happened prior to the events of Pokémon: The First Movie, and happens to take place during said movie. The story is told in brief summary by the harbor manager, Miranda.
Prior to the movie
Before the events of the movie, a fierce storm had—perhaps out of nowhere—raged. When the storm attacked the town, it claimed all but a few Pokémon's lives (it is unknown if the storm claimed the townspeople's lives as well, but is implied to be so). The Pokémon that did survive became filled with sorrow over the mortal toll, and somehow their tears contained a magical property that restored all who were killed by the storm.
During the movie
This time, the storm came back, but not on its own. This was merely a test to Trainers (later revealed) to see if something like a massive storm would deter them. Miranda had warned the Trainers, even saying that prophets have predicted the return of the lethal storm. Officer Jenny also warned that if they tried crossing the sea during the storm, and the Pokémon were beaten up by the savage waves, the Trainers would have no way to heal them, the reason being that ever since the Nurse Joy that used to work there suddenly vanished without explanation, the Pokémon Center had shut down. Perhaps, in fear of the deaths that might happen to young Trainers that were on the way to New Island via ferry, Miranda had also barred the ferry to the island. However, Ash, his friends, three other Trainers, and Team Rocket (in the hopes of nabbing Pikachu while Ash and his friends were on board) were not held back by this, and they all challenged and braved the storm. Many others had stayed behind, however.