It hadn't occurred to Apollo that his question might be odd; after all, he could answer it easily, but not Rory's version of it. He pauses for a moment to think of how to rephrase it.

"Then, what are the Pokémon who are your companions to you? Do they serve you as their master? Are they friends? Weapons? Tools? Experiments? Protectors? Family?"

He maintains his calm tone, even when he lists less pleasant examples. Though after saying that he realizes that he probably shouldn't have added the examples and kept it as open-ended as possible.