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Dang alright here we go.
I would pick up a new mon from each route and they would immediantly die when I tried elveling them with trainers, so I was basically forced to just use Palkia the entire time. I picked up Giratina, instead of Mewtwo, from the cave. The first Pokemon I got on the route to Red was a Mew, who died shortly after to a level 40 Milotic.
I decided it was a good idea to stock up heavily on full restores, and it definitely was. Red had a full team of 80+ dragon types. I don't know how, especially considering since Palkia basically became a HM slave by the end of this run, but I did it. I notice my Pokedex says 25 Pokemon caught, but I only have 20 Pokemon up on the thing, so I must have forgotten some poor lost souls during the nights they must have died. I'm pretty sure one was a Tentacool and another was a Pidgey.
