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Questions on winning plot;
When you first meet admin#1 and grunts get away, do you battle him while the grunts escape? Or does he show up and they all escape together?
And so there is no plan yet on the Golems & Pixies, just that they will be post game?
---WARNING---
Below is what I could possibly see happening, nothing has been voted on or is confirmed in anyway.
In my mind I could see the Admins escaping the authorities and then you would find the three of them in different locations around the region. Maybe Admin#1 on the Sunken Ship near the Oil Rig with Erion. Admin #2 in the jungle near the Safari Zone where the fire happened with Eronze. And then Admin #3 Hiding in the desert with Erace or close by Vivace. Maybe they are trying to capture the Golems themselves at those points but you show up and they battle you first, that way when they run off you can battle/capture/defeat the Golems yourself.
The Spirits would be back near where the Evil Team found them, Yacuma in a Dive spot near Oil Rig, Machima, in the Oasis/Desert Cave, and Patama in the Deep Jungle/Jungle Temple.
Xochi could be found in the Temple where the Orbs were being kept.
Xotec could be at the Temple where Quetzar was originally at. Maybe there is a secret passage in the temple leading downwards, with tough wild Pokemon, and maze/puzzles like strength puzzles and such. And once you reach the bottom you are brought into a room with Xotec, some Ruins, and a Gold Statue(of the Evil Team Leader who escaped by going further into the Temple from earlier in plot). You are able to battle/capture/defeat Xotec, and if you read the ruins they tell of a City of Gold being buried, and anyone with bad intent tries to uncover the gold they are transformed into gold themselves. If you interact with the Golden Statue, it says that the person looks very familiar and a golden nugget breaks off.
Quetzar can change form by taking it to the top of Spiral Pillar, or a place in the Space Cave by the Observatory.