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Is there any glitch or reason one of the Legendary Beasts can just... never spawn? I know that sounds ridiculous, but I'm at my wits end here - I encountered Raikou in 3 hours, and I'm going on 4 months here looking to just encounter Entei, with 0 progress. I did do the box change cloning glitch for another Master Ball (because actual catching Raikou was a whole other adventure), but I can't find anything other than the attempted clone Pokemon vanishing or corrupted saves. Someone told me if they Roar they can disappear, but again, I haven't encountered it at all. (Although I think that's only in FRLG?)

I didn't want to ask this because it sounds stupid, but I just can't believe RNG can be this terrible for anyone, even me... can it...?

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No clue for your case.
I've been playing FireRed and LeafGreen for seven years, tho, and I've never had a legendary beast disappear, ever.
The roar glitch does, indeed, apply to Fire Red and Leaf Green only, not Crystal. If you jacked with the game enough that you corrupted the file though, then maybe you glitched the mechanic, but I doubt that. You probably just need to be more patient.
@FlappersFlappers Are you implying 3 going on 4 months of actively searching isn't being 'patient'?
I never said it wasn't. I just said you might need to be even more patient, though I suppose that was unfair... I tried to do some research but nothing came up, not even for a glitch that could do this. The only other thing I could think of was that the RNG was that bad, but I know that just because I can't answer it doesn't mean nobody else can (hence why I wrote that as a comment). I do think it's really weird that you haven't seen Entei once. Would it help if I gave you some sources of places where you could report this oddity in the case that it is a glitch or something of that nature? There are some threads out there where people discuss issues they came across in their Pokemon games and other people can try to help.
In hgss, if you kill the roaming Pokémon, it will reappear if you battle the elite 4. I don’t know if this applies to crystal, or if it would do anything in this situation, but you should at least try it and see if Entei starts appearing.
@thecarnapper5 Legendaries don't respawn after being the E4 in Gen 2.
I think what he meant was that in HGSS the beasts will disappear after 100 hours of gameplay, but will start roaming again after you beat the Champion. You will know when this happened because their icons will no longer be on your map. From my research though, this doesn't apply to Gen 2.

1 Answer

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No. That is impossible. Entei will stay till you KO it or catch it.
Scource: Waiting ages to catch the legendeary beasts

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Your source isn't relabable IMO, since, there could easily be glitches that the legendary beasts could run away, and
never come back.
If the answer is just yes or no with no added explanation, it’s against the rules, so this is fine.
Actully, it would be well known by now, if you could not catch entei since then it woudl effect your ability to cath ho-oh, which would make people mad
Really? So you're saying there's a 0.0% chance anything possibly could be wrong in the second most glitchy games in Pokemon aside from Gen 1 itself? That using 297 Max Repels minimum a day, for going on 4 months, using multiple different Routes & methods, with not a single Entei encounter, is just 'bad luck'?
Wait, there's your answer, Soundwave! If the Pokemon leading your party is of a higher level than the beasts then it's the Max Repel that is keeping it away! https://gamefaqs.gamespot.com/boards/375087-pokemon-crystal-version/44567106