Kuusou Kagaku Sekai Gulliver Boy

A boy named Gulliver possesses magical abilities and is sent to a magician school against his wishes to develop them for the city's protection. He escapes and later discovers his hometown has been destroyed by the forces of the villain Judau, who kills Gulliver's father and vows to kill him too. Gulliver and his friend Eddison rescue a girl named Misty, who is fleeing from Judau. Joining them are a fairy named Phoebe, a lone wolf ninja called Gecko, and an ancient ship. Together, they embark on a journey to defeat Judau and uncover the mysteries of Atlantis.