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I was following this guide to get to Shaymin and after saving by talking to the Pokemon Center nurse and soft resetting (skip to around 9 minutes), I was supposed to end up in the Mystery Zone. However, when I reloaded (by both closing out of the game and by soft resetting), I ended up on Newmoon Island. I was able to correct the glitch using the video and attempt the glitch from scratch, which got me to Shaymin, but I'm curious about why this happened.

I had previously used this glitch to get to Darkrai so I'm assuming that had something to do with it, so is that why this happened or is there something else I'm missing?

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im thinking this may not be answerable as we have no idea what you did exactly, and it's uncharted territory. like, you couldve made a wrong turn somewhere. unlikely, but i just wanted to mention it
To get to the Pokemon Center nurse, I don't think it's possible I made a wrong turn because they were simple directions that I made sure to follow thoroughly but I can see how this may not be answerable.
It worked on your second attempt, right?
No, I went to Newmoon Island twice. I was never able to warp to the mystery zone by directly entering the Pokemon Center, I was only able to go there by correction the glitch and doing it from scratch.
In that case, can you try again and show us a video if you end up on Newmoon Island again?
That might take a bit for me to get around to, but if I have the opportunity to I will.

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