Throughout Ruby/Sapphire, you will encounter either Team Aqua or Team Magma multiple times doing various deeds in order to further their plot to catch Kyogre/Groudon.
Seems simple enough right?
And indeed the weather legendary plot really is that straightforward. However, some of the details suggest that they also had a backup plan in case Kyogre/Groudon didn't work out.
When the player character first arrives in Lilycove City, they are unable to Surf east from the town due to a Wailmer blockade. A grunt from Team Aqua/Magma is seen standing in front of them telling Wailmer to leap out of the water.
It is easy to assume that he just wants the Wailmer gone so they can leave. But you could also come to the conclusion that he is actually TRAINING the Wailmer in order to get one to evolve into a Wailord. Keep this in mind.
Later on in the game, Team Aqua/Magma steals a submarine. They use it to go to the underwater cave where Kyogre/Groudon reside, obviously. But if you remember the original intent of the submarine, things become less clear.
Captain Stern wanted to use the submarine to look for a "rare deep sea pokemon." The only thing fitting this description is Relicanth, considering how common Chinchou and Clamperl are. Since the submarine was designed to look for Relicanth, it would be easy for the team to casually pick one up on their way to the underwater cave.
Now when you combine the Wailord from their training in Lilycove and the Relicanth from the submarine, Team Aqua/Magma has the necessary tools to open the Sealed Chamber.
My theory is that Team Aqua/Magma devised this clever backup plan to capture the Regi trio in case they were unable to catch Kyogre/Groudon.
What are your opinions?