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I was abusing the RNG sometime in Ruby Version to try and get Rayquaza. To date, that is my favorite Shiny ever since I looked up its cool sprite on Bulbapedia. So, you know, I decide to abuse the mechanics - damn it, I was GOING TO GET that thing legitimately! >:)
It took dozens of hours, but I finally reach him. Sadly enough, I had already used my Master Ball on Latios - for good reasons, obviously - but I had False Swipe, so no problem, right? Well, one critical hit later, my Sceptile is KO'ed and my Revive stock was shockingly empty. That's odd, even for me - in most games, I tend to have at least 10 of all status items, even the unneeded ones.
So, crap. Rayquaza has barely lost half its HP and Sceptile was my ace in the hole. So I decide to send in my status Pokemon - a Butterfree traded from LeafGreen. I had planned to Stun Spore him earlier, but there didn't seem to be much point - I thought this to be a guaranteed shot. I opt to go ahead and Stun Spore - or so I think! I ended up using PoisonPowder. Ah, the eternal anguish I felt at the moment as I saw the PSN marker move onto Rayquaza's HP bar! T_T I almost gave up right then, but, no! I decided to go ahead and just keep throwing Ultra Balls (those I had 99+ of), later resorting to my staller Pokemon in Blissey (also traded from LeafGreen). In the end, it never worked, my Ultra Balls all failed, and my first Shiny Rayquaza flew off into the distance.....
I eventually caught another though. It was a few weeks later, but, nevertheless, this easily tops my most depressing Pokemon moments.
Every wound a new opportunity, every curse a new challenge. I shall encounter defeats... But I will not be defeated.
I found a shiny zubat in ruby in that underwater cavern where you fight team aqua/magma. I had 30 ultra balls and not a single one managed to catch it...
That is horrible luck.
I found a shiny Magikarp back in GSC and, unlike most of the stories here, I actually caught it. The sad part was that in my naive 8 year old mind I thought that a yellow Magikarp obviously meant that it would become a yellow Gyarados. My plan was to breed it with a blue Gyarados to make a green one and then again with the Lake of Rage Gyarados to make an orange one. Then I would have bred the offspring with the parents and each other and so forth until I had a motherf***ing army of incestuous, rainbow Gyarados. Boom! Instant coolest kid on the block status.
But then the damn thing turned out red and made me sad.
I lol'd because that's a clever thought process & the end result WOULD be really epic.
In Heart Gold I was training for the E4 in Victory Road and encountered a shiny Graveler. I had a Lanturn out and decided to switch out to Dragonair to use Dragon Rage to guarantee I wouldn't knock it out.
I forgot that Graveler had Selfdestruct :(
Little tip; any legitimate wild Graveler will know either Selfdestruct or Explosion, without fail. That's how their movepools are put together.
Sapphire: Found a shiny Lairon in Victory Road but I didn't notice it was a shiny, after staring at its red eye for awhile I wondered, is this actually a shiny? I went to look at my aggrons status screen to check his eye colour but sent him out by mistake. I noticed a blue eye and got excited to only be roared away by Lairon.
Again in Victory Road I found a shiny Hariyama, but while attempting to catch it, it whirlwinded me away.
Leafgreen: Found a shiny Rhyhorn in the Safari Zone, it fled.