After the world population and economy is devastated by simultaneous hyper-hurricanes, many different factions and fledgling nations appear. In Japan, an elite class called Logos appears, controlling special zones in the country which have most of the wealth and resources. The Logos exercise control over the Levinas, the lower class which struggles day to day in order to stay alive. The Levinas are restricted from entering the special zones, causing tension which creates a resistance group which fights back against the Logos.
Sana is being chased by what seems to be an army, and Jil is helping her get away. The two make it very far and almost reach their destination until they are surrounded. Jil realizes that they are about to be captured, when all of a sudden someone begins attacking to army. His name is Jo and he barely speaks, but he knows Jil pretty well. The three of them later leave the city, with a little man named Goro tagging along. Goro seems to have sources of information.
Jin and Jo go to an abandoned super market to get good before they leave. While Jin's inside, some police men come across their truck... But Jo easily handles that. As they're making their way across the ocean with Goro's help, a pirate ship appears from the sea and blocks their path. It turns out that Goro was trying to steal their military attire from the start. To make matters worse, the military shows up.
Jin and Sana are separated from Jo and taken aboard the pirate's ship, where they meet with the leader, an odd man named Toraji. Toraji seems to know a bit about Sana and the Phantom organization. Meanwhile, Jo forces Goro to help him find Jin and Sana.
We learn that Toraji was a former member of Phantom as weel, but he left along with one of ther submarines. Jo comes aboard the ship the save Jin and Sana, and in the end Toraji tells them to go meet a man who will surely help Sana.
Jin, Jo and Sana finally meet up with the man Toraji told them they could trust, and we learn that Jin planned on meeting him all along. The man is Sana's grandfather, and we learn that her father was a skilled doctor before he was murdered. Jin knew him very well. As sana and Jin taslk, Jin reveals that his father took his own life, and that he saught revenge on the men that drove him to it. Jin and Sana play the piano together, and Sana suddenly collapses
Members from Phantom invade the town where the three are hiding seeking Venus. Meanwhile, Sana awakes after collapsing at the piano. Suddenly an alarm goes off. Jo and Jin fight back to protect Sana.