The answer to this question has been revealed in the Pokémon XY series.

In the anime/manga fan community, there are many peculiar questions surrounding beloved works. Pokémon is no exception. For example: 'Can a Pokémon catch another Pokémon with a Poké Ball?'.
This seemingly difficult question has an answer, found within the Pokémon anime, illustrated by the actions of Pikachu and Meowth.
In an episode titled 'A Frenzied Factory Fiasco' from the Pokémon XY series, the storyline unfolds with Team Rocket taking control of a Poké Ball factory. They lure Ash and his group into a trap, with only Pikachu able to escape. During the escape, Meowth attempts to catch Pikachu with a Poké Ball.

The intense chase leads Pikachu and Meowth to the assembly line of the factory, where various types of Poké Balls are manufactured. In a decisive moment, Pikachu uses a Luxury Ball to try and catch Meowth, successfully doing so. Meowth is ultimately sucked into the Poké Ball but manages to escape after a while.
This incident not only highlights the first time a Pokémon uses a Poké Ball to resist another Pokémon but also proves that this process is similar to how trainers catch Pokémon. While Meowth isn't fully caught, the episode suggests the ability of Pokémon to control others through Poké Balls.

A similar example occurs in the movie 'Mewtwo Strikes Back'. Mewtwo created its own Poké Balls to catch and clone Pokémon. However, Mewtwo does not command the captured Pokémon like a trainer.
The interaction between Pokémon and Poké Ball paves the way for various theories, such as humanoid Pokémon commanding a team consisting of other Pokémon.
