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Pretty dark question.

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The link below has a list of deaths. I haven't read it, but I'm assuming that it's mostly major characters. Also, are you looking exclusively for characters that were shown alive but then died later, or just everyone mentioned to be dead?
https://bulbapedia.bulbagarden.net/wiki/Category:Deceased_anime_characters
who were shown alive but died later

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Best answer

Sir Aaron (Lucario and the mystery of Mew)
Aila (The Legend of X, Y, and Z!)
Amber (Mewtwo strikes back)
Captain (Orange League EP095)
Chapman (XY108)
Conley (BW137)
Cubone's mom (File 2: Pokémon Origins)
Damos (Arceus and the Jewel of Life)
Dr. Fuji (Mewtwo strikes back)
Ghost of Maiden's Peak (EP20)
Ghris (Hoopa and the Clash of Ages)
Godey (The Rise of Darkrai)
Groudon (Jirachi: Wish Maker)
Jan (The Legend of X, Y and Z!)
King of Pokélantis (AG178)
King of the People of the Vale (White- Victini and Zekrom and Black- Victini and Reshiram)
Lacy (XY014)
Latios (Pokémon Heroes: Latios & Latias)
Lon (XY072)
Lucario (Lucario and the Mystery of Mew)
Marcus (Arceus and the Jewel of Life)
Marcus's soldiers (Arceus and the Jewel of Life)
Nikola (Volcanion and the Mechanical Marvel)
Olympica (The Legend of X, Y, and Z!)
Queen Rin (Lucario and the Mystery of Mew)
Stoutland (SM021 ;()
Tapp (Arceus and the Jewel of Life)
Veofum (The Legend of X, Y, and Z!)

Source: this, and the sad SM episode ;(

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edited by
2 votes

There are 27 official character deaths in the Pokemon Anime and movie series. This includes both Humans and Pokemon.

Here is a list of all of the deaths: https://bulbapedia.bulbagarden.net/wiki/Category:Deceased_anime_characters

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Just realized Hellfire commented this a few minutes ago. Sorry!
what aboutat about gary's raticate?
no one can prove we did that. riiiiiiiight, officer jenny?