Who is the God of the Pokémon world? Arceus is often credited as the creator of the world, with other Pokémon, such as Palkia and Dialga, being responsible for other elements of the universe like space and time. However, the world of Pokémon has a few oddities that put into question this established lore. Specifically, the fact that the story of Noah's Ark also exists in the Pokémon world.
There are many cases in the early days of Pokémon where the lore would contradict later established canon. The most egregious of this, however, comes in Episode 16 of the Pokémon anime, "Pokémon Shipwreck." The episode references multiple ship-based disasters, most notably that of Noah's Ark. However, while this story might seem like a huge contradiction to the established lore, there actually may be a canon explanation for why the Biblical story exists in Pokémon.
The Episode
"Pokémon Shipwreck" is the second part in a series of inter-connected episodes centered around the S.S. Anne. In the previous episode, the brawl between the members of Team Rocket sailing on the S.S. Anne (not just Jessie, James and Meowth, but the entire organization) resulted in the ship capsizing and sinking into the sea. While everyone else was able to escape, Ash, Misty, Brock, Pikachu, Jessie, James and Meowth are stuck on-board and presumed dead. Officer Jenny even holds a funeral for them.
However, the group survives and attempts to escape the ship. This leads to multiple references to famous maritime disaster stories, such as the Titanic and Noah's Ark. While the Titanic is a historical reference made by the series' narrator and thus isn't referenced in-universe, Brock actually references Noah's Ark specifically to describe their predicament. This indicates that the story of Noah's Ark exists in canon.
Why Does Noah's Ark Contradict Established Lore?
The story of Noah comes from the Judeo-Christian tradition. Noah is contacted by God and told that humanity, for its continued and egregious sins, is going to be destroyed in a massive flood. However, because Noah and his family are truly good people, he is tasked with preserving humanity by placing two of every animal into a massive ship he is to construct to endure the flood. He manages to preserve a seed of civilization before the flood comes.
While Judeo-Christian iconography is all over Pokémon (a few episodes after "Pokémon Shipwreck," Misty brandishes a cross on a Gastly), there is little direct reference to Biblical stories or figures. They do not reference God, Jesus, Abraham, Israel, Satan or any events relating to them. So if the belief system itself does not exist in Pokémon canon, where would an individual story from it arise from?
Furthermore, Noah would have had to collect every single Pokémon in the world twice over -- making him, effectively, the world's first Pokémon Master. Or perhaps just bought one of each gender and a LOT of Dittos.
So Who Made Noah's Flood?
However, let's remove the Noah story from Judeo-Christian ideology. Suppose there was a massive flood that required someone named Noah to collect the world's population of Pokémon on an ark. This begs the question: what caused Noah's flood?
Arceus has a very detached role in the lives of Pokémon and humanity, instead sending his various other Pokémon creations to manage life on Earth. Ergo, it's unlikely that Arceus itself conjured the flood. However, there is one legendary Pokémon that canonically can create a flood that can drown the entire planet.
In Pokémon Ruby and Sapphire, we are introduced to Kyogre and Groudon. Both Pokémon have the ability to alter the weather patterns of the planet, with Groudon drying out the planet while Kyogre conjures a great rainstorm to flood everything. It's only when Rayquaza interferes in the two Pokémon's eternal war that balance is struck on the planet.
In canon, however, Kyogre did actually create a massive flood similar to the one Noah endured in the Bible story. Quoting its Pokédex entry from Sapphire, "Kyogre is named in mythology as the Pokémon that expanded the sea by covering the land with torrential rains and towering tidal waves." This right here establishes that Kyogre did indeed create a legendary flood.
If we come to understand that Noah endured a flood created by Kyogre rather than the Judeo-Christian God, the story of Noah's Ark seamlessly integrates with Pokémon lore. While it's unlikely the writers of the anime could foresee Kyogre's existence years before the release of the Hoenn games, this reference adds a sense of coherency, further mythologizing the legendary Pokémon in exciting, interesting ways.