My brother failed to save before battling the legendary (Groudon), and saved afterwards when his team had been wiped out by Groudon. Upon returning to the Cave of Origin, to the same spot that Groudon first spawned, he is not there. What can be done to make him respawn so he can be battled again, in order to advance in the story?
3 Answers
If you got wiped out by your legendary during the story, renter the Cave of Origin. On the second floor when going down, there is the normal stair-case, as well as another entrance to the west. Take the entrance and keep going downwards that way. You should eventually be able to encounter your respective legendary in another room.
Source: thanks to the user "[Dark Star] Greninja" on pokemondb.
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1+1 Also, now that you mention it, I kind of recall having paths splitting up and saving right before there. I guess I forgot to go back and check out that other path after I had beaten Groudon...– JerryCommented Jan 7, 2015 at 12:30
Where you find Groudon is when it takes you somewhere and you battle its Primal form, right? If memory serves me right there's another way you can go in the cave that leads to where the actual fight happens. This other way is blocked off until Groudon/Kyogre take you to where the actual battle occurs but since you've done that scene it should be fine.
You can rebattle any legendary you havn't yet captured, whether you kill it or get wiped out. Just defeat the elite four again and the legendary will reappear where it naturally lives, or if a moving pokèmon, starts teleporting again.
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1The only problem with this answer is, he can't challenge Gym Leader William if he hasn't first caught or defeated Groudon/Kyogre. Without that last badge he can't even challenge the Elite 4. Your answer is therefore not the correct one.– NolonarCommented Jan 11, 2015 at 1:23