PokéBase - Pokémon Q&A
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We all know that Ash has scanned many Pokemon he has seen before twice. Of course, this has been done each region and rarely twice in the same region. Now the question is: Is this the SAME (but upgraded) pokedex he has received in episode 1, or does he get a new pokedex every time he begins a new region (like trainers do every time they start a new game and have to catch the same Pokemon again).

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2 Answers

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Im pretty sure they get a new one because in the first episode of the now series Pokemon X and Y, he gets the Kalos region pokedex from Professor Sycamore. What he does with them I have no idea. Maybe he gives them back to professor oak or something idk

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The pokedex is probably included in the anime to create a relationship for viewers between the show and the game. The fact that they based the anime around the journey of a trainer must mean that they wanted their audience to be as fully immersed into the story as possible.
So my guess about what ash does with his pokedex is probably the same as what happens to the pokedex in the game. nothing. except for supplying ash with information about the Pokemon he encounters. but just like the pokedex in the game, it is probably pointless.

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