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Well dang everybody.
I finished up half of the Crystal Clear N-Locke here and this is what went down. I'll get a template going later.
Basically, I started in Johto with Togepi, proceeded to every gym with with a group of mons that were caught in the surrounding area. Each mon that survived the gym or partook in the battle in some meaningful way was then boxed, with the exception of a couple which were used to catch the next mons and fight trainers along the way -- this was risky, but it meant that I trusted in these pixels! For the E4, I create a team out of the mons that won badges.
The first team consisted of Togepi (fought in Gym 1), Starmie (Gym 5), Kingdra (Gym 8), Ariados (Gym 4), Hypno (Gym 3), Golem (Gym 8). However, we got slapped by the 4th E4 with his Lugia! It was sad to see Togepi and Starmie, who both had been major players in their gym fights and between routes, rounding up mons.
The second team consisted of Kingler (Gym 6), Umbreon (Gym 3), Noctowl (Gym 3), Steelix (Gym 2), Girafarig (Gym 7), Slowking (Gym 2). Everything was going fine until I lost Slowking to the 2nd E4 to a critical. Then Nes, the Girafarig took a chance to paralyze the 4th E4's Lugia, which it did! But then died to a critical Aeroblast. Umbreon then cleaned up with Confuse ray, Toxic and its bulk.
Finally, the Champion, ShockSlayer, the dev of the hack was all that was left. Lowe, the Steelix had the chance to set up Curse and took out many of the steel types, but stupidly, I left it in against a Magcargo thinking it would be faster! It couldn't dodge a Fire blast and a really useful bro was dead because of my mistake. Shoe the Noctowl, hypnotized some foes along the way. Then Georgina, the Kingler swept the rest of the team with critical Crabhammers.
Overall, I had a lot of fun with this run as an N-Locke, and really glad to have heros like Kingler, Umbreon and Noctowl added to the hall of fame.
But the run is only half-over and I need to do the same for Kanto!