The events of the story take place 5 years after ZOE: 2167 IDOLO, the events of which are referred to as the "Deimos Incident." The first twelve episodes take place before the events of the first game (Zone of the Enders), while the rest of the series takes place after. The story centers around a space cargo transporter named James Links, his family, and their adventures in the Zone of the Enders universe. The events of the story are set in motion when James is sent a mysterious Orbital Frame called Dolores (a.k.a ISIS) with instructions to deliver it to Earth and not to let anyone capture it. During the series, James attempts to reconnect with his adult children, Leon and Noel, as well as search for his long-lost (and reportedly dead) wife Rachel. The intelligent, well-mannered and well-meaning, but somewhat awkward and naive Dolores accompanies him as many enemies attempt to stop him, manipulate him, or capture Dolores.
