I am sorry to say that this story is... dead.
Not by terms of lack of ideas, rather, lack of flow.
Not only did I not have an end point for this story, nor could I come up with one proper, but I've lost all faith for this being worth reading.
However, for the... less than one of you out there who wanted to see this stories end, I will present to you the synopsis for the rest of the story. Because I hate to leave such a work out in the cold.
The story was going to progress through a city, where a major mafia lord takes an interest in Bagi for her rarity, and wants to add her to his collection. However, Bagi attacks and kills his personal guard as well as brutally crippling the drug lords leg. Ryo has a hard time getting her to calm down, and, as they go, she seems to be getting more aggresive, more than the 5 years later in the original movie. She stays loyal to Ryo though, and he's quickly becoming the only ground she has to reasoning.
They make it past the rest of the Mafia goons to the hanger, where they steal a private jet. But since nither of them know how to fly it, it goes pretty badly, and gets shot down by some local police officers. They make it out okay using some parachutes. However, they're caught by the police. One of the translaters is broke, and the other one is with bagi, who is kept separate from Ryo. Ryo steals the keys to his cell as well as a gun from an unsuspecting guard, and breaks out of jail to go rescue Bagi. The government was going to acution her off, but by taking one of the officals hostage, Ryo delays the auction just long enough to break Bagi out.
They steal another plane, and, by chance, are able to fly it all the way to america. There, he is able to communicate a fabricated story to law officials there. He is able to get him and Bagi deported to japan, where, they get a break for a while. They decide to stop the experiments from taking place in the super life center. After a month of travel, they make it back to the center, where they planned to confront the CEO. However, before they can talk him down, Bagi attacks the CEO, killing him. She then turns on ryo for a moment, until he reminds her of who he is.
Though fearful of what bagi might become, he vows to rehabilitate her. They burn down the super center, and live in the wilderness for 3 years while Ryo reteaches Bagi. They eventually return to civilization, Bagi fully re-taught having managed to fight off whatever Ryos mother gave her. They live their life in peace as husband and wife.