Ginga tetsudô Three-Nine: Eternal Fantasy (1998)

Tetsuro believed he was freeing the Earth from the clutches of the Metanoid Empire’s tyranny. Yet one year after his return, Tetsuro is a prisoner of a new tyrant, and this one human! However, before worse than imprisonment can happen to the boy, Maetel and the 999 swoop into the boy’s rescue. With his freedom, gun, and trusty hat returned to him, Tetsuro reaffirms his desire to save his home. But a new darkness is rising to swallow the light, and one of its agents has him in her sights. Before the train can depart for a new destination, Tetsuro will have to face the deadly knight Helmazaria!