So Archie was all like, “Kyogre! Listen to my commands!” And Kyogre was all, “Haha, whut?” That’s pretty much the plot to episode eight of Pokémon Generations, “The Cavern.”
It’s also the plot of Team Aqua, the group which, depending on if you’re playing Sapphire or Alpha Sapphire, wants to make the world better for water Pokémon AND humans by raising the sea level or the same thing only without the humans part.
A note to evil or misguided organizations: if your plan involves raising the sea level, no matter the intentions, it’s a bad plan. The only worse plan involves forcing Kyogre to undergo Primal Reversion and expecting it to listen to anything you have to say afterwards.