Chiteikoku no Kaijin

Chiteikoku no Kaijin is a science fiction manga depicting the struggle of boy-scientist John and his friends against people of the underground, who are plotting to take over the Earth.

John invents a safe, high-speed, earth-penetrating train to fulfill the final wishes of his father, who died in a plane crash. One day John meets Mimio, a rabbit with human-like intelligence, and together they head to the center of the Earth in the newly completed rocket train.

But when they get there, they discover an underworld ruled by a queen who plots to conquer the Earth. John and his friends, including Uncle Bill who comes to help, somehow escape back to the surface. They make another rocket train and return to the underworld.

(Source: tezukaosamu.net)