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The commander was present with the Rockets who were occupying Pokemon Tower. He is likely the grunt who uses two Zubats, a Ratatta, and a Raticate, as that Grunt is fought last.
Pokemon: The Origin
The commander and his team were once told to capture a group of Pokemon in order to sell them. They nearly managed to capture a Mankey, a Raticate, a Sandshrew and a Sandslash, and failed to capture the baby Cubone they were after (they wanted to sell his skull) due to the intervention of its mother. Infuriated, the commander killed Cubone's mother - Marowak - with his electric staff.
Control of Lavender Town
The commander and his team arrived in Lavender Town, where they took control over the Pokemon Tower to use as their headquaters, with the commander using the Silph Scope to get past ghosts. Eventually the commander fought Blue and was defeated, he and his team left after one of his grunts was defeated by Red.