Leonardo Da Vinci announces that he is going to unveil his latest work in San Marino. Its title is "World Harmony." After the announcement, for some reason, people all around the Italian Peninsula fall unconscious... and Lupin and the gang are no exception. Lupin later awakes in San Marino, and in front of him, he spots Da Vinci. As he follows the artist, Lupin discovers what "World Harmony" actually is!

Three people, including Hiromi, were murdered the first time around, but this time, the targets were moved out of the killer’s sights. However, Satoru is worried about whom the killer will go after next in place of his intended victims.

Having experienced the Great Ninja War as a young child, Itachi constantly questions the meaning the life and death, distancing him from other children his age. Soon after entering the Academy, Itachi exhibits his genius and finds himself at the top of his class.

After Nagano Prefectural Police Inspector Takeda is murdered, Lieutenant Kano is found dead from hanging in his home. From the body's condition, Inspector Morofushi reasons that after being strangled, the body was hanged from the ceiling by someone. Later, the culprit sends an e-mail declaring that he will kill three additional people. Segreant Akiyama is called to Mt. Saijozan by the culprit and is dragged off a cliff by a car. Inspector Yamato's fingerprints are found on the rope that was wrapped around Kano's neck, and Section One Chief Kuroda puts out a BOlO for Yamato as the suspect who murdered three men...

Sasaki Isaburo's past with the Shinsengumi, Matsudaira, and Imai Nobume is finally revealed.

It's Daichi's turn in the pilot chair, but he's not concerned about himself. Instead, he makes a decision that mirrors what his father did, all those years ago.

Chizu has been chosen, and she's determined to do one last thing before she completes her role as a pilot of Zearth.

With Kako dead, but the enemy still around, the next pilot needs to be selected. As the chairs spin, Chizu recalls her past and what led to her being where she is now.

The next pilot is Kako, but the other kids can't find him, though Chizu has an idea of where he might be. When the next enemy appears, the military makes an attempt a first strike.

The children realize just what it means to be chosen as a pilot for Zearth. Meanwhile, the adults finally make their move, as the military gets involved, both with Koyemshi, and Zearth itself.

Masaru's family life has made him come to divide the world into two types of people: those born to die, and those born to survive. When it's his turn to fight to protect Earth, which type will he end up as?

Questions remain in the wake of Takashi's death, the most pressing of which being, how did Takashi die? Both the kids, and the police, want to know. Amidst the grief and uncertainty, the next pilot is chosen.

The final fight is upon the Earth. Jun, as the final pilot, fights with the whole world looking on, and with everything he's learned guiding him.

Jun and Yoko's plan to fight against Koyemshi goes into action. The thirteenth battle begins with Yoko as the pilot, and the government enacting their own schemes to deal with the enemy.

Jun takes Kana back to her father, and asks Yoko to go along with them. Along the way, he thinks upon his life until now, and ultimately comes to a decision about Koyemshi's offer.

Kanji's turn to pilot Zearth is marked by a strange setup, wherein the enemy appears to be targeting the Chutenro Tower research center. In the course the fight, they discover the ultimate purpose of this endless game.

Swayed by years of guilt and hopelessness, Yoko finally comes forward and speaks, telling the story of herself and her brother, who is now known as Koyemshi, and the endless cycle the two are in.