James Links, a former military man, is now in the transportation businesses. He has two grown children, Leon and Noel, and he had a wife named Rachel who passed away. James continues with his ordinary life until one day he meets a highly-advanced Orbital Frame with an A.I. of unknown origin - Dolores! Now, James is in for one heck of an adventure

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James, Leon, Noel, and Dolores attempt to escape toward Mars, where they suspect Rachel is.

Realizing that there isn’t enough fuel to reach Mars, James must make the ultimate decision... that is until Dolores stumbles across a hidden space station!

After a scuffle with a satellite, James, Noel, Leon, and Dolores hide out in a garbage dump right outside of Mars. James soon comes up with a plan to hide their ship in garbage and try to enter the atmosphere, hoping to be undetected... that is if they can pull it off!

James, Leon, Noel, and Dolores land on Mars at last. They are "shipwrekced" in the ocean and are rescued by two people who have made it their job t protect Mars and its progress into a new "Earth". Little does James and the others know, they have just landed into a conflict between their new friends and the group opposing them.

James and company manage to find land. After surviving the harshness of a Mars night, the four find a "greenhouse" with oxygen and two people. Who are the old man and child and what are they doing there? And, what will happen when the greenhouse comes under attack?

After defeating a mech, James opens up the cockpit and discovers that the pilot is actually a young girl named Rebecca Hunter. She attempts to blow up the mech, killing both of them, but James manages to escape, saving her in the process. With Dolores, the three head to an abandoned Energy Plant. There, James treats Rebecca with kindness, giving her food and allowing her to take a bath. However, she soon manages to cut off all the power and escape with Dolores. Will she make it back to her squad? Will James survive without any oxygen, or will he find a way out?

James, Rebecca, and Dolores attempt to find humanity. They eventually do, although it isn't whom James expected. Can James shake Rebecca's friends and still manage to drop her off safely? Meanwhile, Leon and Noel find a town thanks to a man named Nikolai. But, is he friend or foe? And, what plot does Cindy have in mind?

Rebecca is back at the base, but all is not well. A powerful man comes and challenges her to a duel. It is interrupted, however, when the Earth forces arrive looking for James Links. Afterwards, Rebecca visits an important woman.

With barely any fuel left and a dearth of oxygen, James volunteers to trek in the sand storm for 24 hours to the next town. The good news is that he stumbles across a town less then half way. Even better, he meets his idol Isaac Barrett in the town. But, the good times are short lived.

Nikolai captures Noel and challenges James to a duel. Will James be able to win? And, why does Nikolai hate James so much?

The Links Family finally come within feet of where Rachel is. James and Dolores cause a massive distraction, as Leon and the others sneak in and track down Rachel. Will they find her? And, will everyone be able to escape alive?

Rachel fills the rest of the gang in on the situation and what Dolores actually is. Menahwile, Naphth Pleminger learns that Isis is now calling itself Dolores. Upon hearing this, Naphth gets angry, proving that he may be more then who he seems.

War has begun! Leon figures out their plan via Nikolai's left over files. With the information at hand, can the Links family pass it on to the Earth Forces? And, when James and Dolores head out, what trouble will they find? Civilizations are still present, yet a battlefield surrounds them.

After Sameji overthrows Van, James and Radium face off. What is Radium's plan? Will James win against him, or is he just walking into a trap?!

After waking up in a hospital bed, James informs everyone that Radium intends to drop the orbital elevator on Earth. The only way to stop him is to convince Earth and Mars to cooperate with each other. Will James be able to do it? And, with Dolores still out of commission, can James bring her back to how she was? Is there hope? Or, will Radium succeed?

James and the crew head toward Earth in hopes of catching up with Radium. However, when they get close, they discover that it's too late. James goes on ahead with Dolores and the two enter in the middle of a fierce battle. Meanwhile, Leon is put in charge of the ship and must make an important decision.

James manages to save Rebecca, and Dolores saves James. James lectures Rebecca, attempting to open up her eyes. Will he get through to her? Does he even have time? Meanwhile, Leon and the others have trouble of their own, as they have to purge two levels of the orbital elevator to maintain balance. What's worse, they have to do it manually! Will Leon and Noel succeed? The situation is dire, as James and Radium face off! Who will be victorious?

James and Radium's fight comes to a thrilling conclusion. With that all said and done, however, the end is not near. The elevator is still descending, and at this rate, there's nothing that can be done. Dolores decides to take matters into her own hands and sacrifice her own life to stop the elevator from falling! Will she go through with it? Will her power be enough? Will she survive? And, what has become of Rebecca and Axel? The enthralling conclusion of Zone of the Enders has arrived!!