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There are two possible problems here:

1. You made it faint, but did not capture it. If you defeat a Pokemon, but do not capture it in a Pokeball, it will not become available to you.

2. You captured it, but you had six Pokemon already in your party. When this occurs, the Pokemon is transferred to Bill's PC. You can exchange it for another Pokemon in your party at almost any computer.

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Q: You have just beat Rayquaza but it didn't join your team?
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