Earth, eight months after the end of the One Year War. Captain Monica launches a secret mission, "Operation Thunderbolt," and selects Io to pilot the Atlas Gundam. She leads the assault landing ship Spartan into a part of the ocean effectively controlled by the South Seas Alliance. Their objective is to secure or destroy the data of the Psycho Zaku, which the Alliance now possesses. Daryl, who took the upper hand in his battle with Io, has descended to Earth as part of the remnant forces of the Principality of Zeon. He has also been given the mission of obtaining information on the Psycho Zaku.
Fighting alongside his new comrades, Io encounters Commander Peer, the South Seas Alliance's border garrison commander. In the sea, on the ice field, and among the thick jungle, the mobile suits of Zeon, the Federation, and the South Seas Alliance battle each other. The war is not over yet.
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.
A futuristic firefighting mecha service is created to protect the world.
Pirates from around the world gather at the Pirates Expo to join the hunt for Gol D. Roger's lost treasure.