SixaxiS said:
Yet all of them revealed their plans to the very detail so you had absolutely no problem in stopping them. And to top it off,
Cyrus gives you a friggin Master Ball!!! he allows you to ruin his plan with the throw of a single pokéball. Furthermore,
he allows you to release Azelf, Uxie, and Mesprit, who in turn ruined Cyrus' plan.
Bad guys are always supposed to reveal their plans. That's a law.
...And Cyrus didn't need the Master Ball, so why should he keep it (he had control over the Legendary Pokémon after using the Red Chain, so the Pokémon couldn't be captured anyways).
The only thing that stopped Cyrus was indeed allowing the player to release Uxie, Mesprit and Azelf, but Cyrus couldn't know that they could destroy the Red Chain, so he was quite sure he didn't need to hold them captured anymore.
If he knew about that, there's no way he would let the player release the three, and his plans would have succeeded.