The Aether Foundation decided to experiment with some serum for the pokemon, they want to make a better storage system than the pokeballs, all the pokemons that were injected are immobilized and then they are thrown into a production line which crush the pokemon and then they are left in boxes.
Shiny pokemon are removed from the production line to be left somewhere else after being crushed.

Want a second picture where the store is seen? ^w^