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Another long update. I spent about 16 hours with Zeta now.
Did the third Police Club mission. After chasing them out of Pallet Town in the second mission, I have to stop Team Rocket from catching Mew and end up fighting Giovanni himself. They still get Mew's DNA and in the fourth mission I get to their base. After fighting some grunts, Giovanni battles me again but this time he only has a Mewtwo at level 45. After that, Mewtwo kills Giovanni (and all the other grunts) and I escape.
I also discovered a Trainer who helps you train. You pay him and he sends out six Audino.
Following the main game again, I enter Mt. Press to track Team Asgard down. After a long climb Asgard challenges me to a double battle with my rival as my partner. They attack with seven Pokémon, but this battle went better than the last double. On top I fight the Asgard boss himself who is about to awake Jirachi. Surprising level spike here, he also has a lvl 58 moxie Salamence.
Jirachi appears and I catch it. Just when an angered Odin whips out his gun and is ready blow his load into me, Arceus stops him. It turns out that Odin is actually Gold. What a twist! Odin runs away, and Arceus turns out to be the Zoroark of an E4 member.
My next destination is the seventh gym.