Emiya Shirou is a young magus who attends Homurahara Academy in Fuyuki City. One day after cleaning the Archery Dojo in his school, he catches a glimpse of a fight between superhuman beings, and he gets involved in the Holy Grail War, a ritual where magi called Masters fight each other with their Servants to win the Holy Grail. Shirou joins the battle to stop an evildoer from winning the Grail and to save innocent people, but everything goes wrong when a mysterious "Shadow" begins to indiscriminately kill people in Fuyuki.
In the late Middle Age's Italy, Leonardo "Leo" Da Vinci is a young boy lover to invent advanced machines who lives happy with his best friend Lorenzo and beauty Lisa, being secretly fall in love with her. After to test the first dive suit of his creation in a lake, tragedy appears when coming back to home Lisa realizes that her house and lands have been burned by a fire. Owner of the lands threats Lisa's father to marry her with his son if he doesn't give all money he debts as retribution by the fire, causing Lisa's sorrow. Trying to save her, Leo Da Vinci decides travel to Florencia to gain money and pay the debt with help of Lorenzo. Unable to keep the secret, Lorenzo reveals Lisa Leo's plans, and Lisa joins her friends to make the travel to the big city, where they meet a storyteller that explains in a plaza the story of a pirate ship sunken with a great treasure inside it. Believing it as a true event, Leo buys the treasure map to the storyteller, but it's stolen by a rogue and orphan little child called Agnes. Making a deal with her, Leo recovers the map and Agnes joins the group at the same time that Niccoló, a little child lover of science and astronomy who befriends with Lisa. All five arrive to Montecristo Island looking for the treasure, but not knowing that a pirates follow each step they make, waiting the right time to steal the treasure and eliminate Leo and his friends.