The Flying Ghost Ship (neo1024)

Hayato's home city is under attack from a gigantic robot. His parents are lying dead in the rubble and the only remaining friend is his dog. His only thought now is revenge against the owner of the Phantom Ship (from where the robot said he was sent).
He ends up in the house of Kuroshio, the leader of the fight against the Phantom Ship and the most important person in the city. By complete accident, Hayato finds his way to an underground passageway where he realizes that the true nature of events does not mesh with what Kuroshio has told him.
His life is now in great danger, and only he can stop the plans of the evildoers.