In my story series Cinos Pokémon Chronicles, Giovanni being Ash's biological father have been kept as a secret by Delia since Ash was born an only mentioned him but not by his name.
Giovanni also kept this as a secret toward his organization Team Rocket, none of them especially Jesse, James, and Meowth.
5-6 years prior to Cinos' Pokémon Chronicles: 3 Years Later where Ash is now 13 years old & Cinos is now 22 years old (or 154 in dog years), Giovanni and his organization Team Rocket made a deal and an alliance with The Kraang to create powerful Pokémons by mutating them with the mutagen.
Kraang Sub-Prime who is head of this operation order by Kraang Prime knew that Giovanni had a family with a wife and a child who is 7-8 years old but didn't see them. Until Kraang Sub-Prime encounter Ash, he have a feeling that this boy who claims his father is somewhere else is Giovanni biological son. So where his new Mewtwo mutant is being created, Sub-Prime will use Ash's mother Delia as a captive and will force the truth to hurt Ash's spirit, heart, and mind.
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Cinos' Pokémon Chronicles
FanfictionThe Cinos' Pokémon Chronicles is a spin-off series staring Cinos The Werehog who is in the Pokémon World. Cinos travel with his new friends: the protagonist of the anime Ash Ketchum and the mascot of the game the electric starter Pikachu. Cinos, his...