Pokémon: Rocket Revenant

Enzo has lived a hard life. First, when he died on Earth and woke up as a dirt-poor orphan in Kanto, a world where a Trainer License costs more than a life. Second, after spending fifteen years clawing his way up from a Team Rocket logistics slave to a Squad Leader, only to be betrayed by his own Pokémon during a suicide mission in the stratosphere. Dying in the cold vacuum of space, Enzo gets an impossible third chance. The cosmic entity Deoxys intervenes, downloading a "Virus System" into his mind and regressing him fifteen years into the past—back to Day 1 of the brutal Rocket recruit assessment: Trial Island. — Description from novelcodex.org