PokéBase - Pokémon Q&A
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When you defeat enternatus, you catch it. But what If you have no Pokéballs to catch it with in the first place?

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Well, this has already been answered, but you just get another Pokeball in your inventory.

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If the player has no Poké Balls when they are prompted to capture Eternatus, one will appear in their bag.

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As you see, it's like a must-catch Pokemon.
Hope this helps!

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Thanks!
No problem.