Question

I accidentally killed Deoxys. How can I try again?

Answer 1

You need to re-defeat the elite 4, then head back to the sky pillar and deoxys will be waiting there, like in Pokemon X/Y with Zygarde and Mewtwo. Source

Comments

thanks this really helped. i've been trying for deoxs forever. i even bought two pokemon ranger games but lost one :)

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No problem! I happened to look this up a while before due to me killing deoxys too.... Great minds kill pokemon alike, eh?

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yeah i was trying to be all mocha and use an ultra ball. it worked for rayquaza and kyogrue... this time masterball all the way.

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XD I used a masterball on Kyogre because I was ill-prepared for catching it. So, I ended up having to use False swipe, Yawn, and Ultra balls to catch my Deoxys.

Answer 2

You can try again by defeating the Elite Four again. If you accidentally killed any Pokemon Legendary, it will respawn once you defeat the Elite Four and the Champion again

Source: Experience