Four years after the defeat of the Death Saurer, a Blade Liger is running through a test, and does very well. Van, the pilot, is then called by Colonel Krueger, who tells Van that he plans to retire. Van doesn't want him to, but Krueger tells him that he's taught him everything he can. Van passed the test, and he even did it without an Organoid. At a mine, Dr. D and Fiona are searching for Zoid Eve. They wonder if they'll ever find it.

President Camford recieves a call from Emperor Rudolf about an unknown Zoid, that can travel underground, attacking one of the Imperial bases and now it's in Republican territory. Meanwhile, Van and Zeke arrive at the Wind Colony to visit his sister. Zeke stays at Van's house while he goes to his father's grave. When he's about to leave, he runs into a man with red hair, who calls himself Hiltz. When Van gets distracted by his sister, Hiltz disappears. A Republican base is attacked by the unknown Zoid, and Hermann, flying in a Pteras, determines that it's a Stealth Viper and gets shot down. The Zoid is headed to the Wind Colony.

Van and Zeke visit the ruins where they first met. Then Zeke senses something, a Gustav headed their way. It's Fiona and Dr. D, who is sick, and they're headed to the Wind Colony. Then they are attacked by the Stealth Viper, and Van rushes to help them. He takes them to his house, and after a while Fiona wakes up. She and Van talk about journeying together again, and they look at his father's knife. Then Van hears his sister scream, and he runs off to help her. Fiona follows with his father's knife. Van's sister is being attacked by a red Organoid. Van defends his sister, and almost gets hurt by the spikes on its tail. Fiona tosses him the knife so he can use it, and Zeke comes and charges into the other Organoid. Then the red Organoid hears a whistle, and it flies off, using boosters that emit red energy.

Meanwhile, the Wind Colony is attacked by the Stealth Viper. Van gets there in his Blade Liger and knocks it down, then throws it away from the Colony. The red Organoid then fuses with the Viper, healing all of its damage. Then it releases a thick fog, and Van can't see anything. He gets shot a lot, but then gets up remembering how Stealth Vipers fight. He uses the hot air from his vents to creating copies of himself, because the Viper uses a heat sensor to find opponents in the fog. The Viper shoots at all the copies, and Van attacks from behind. The red Organoid flies out of the Viper taking the pilot with him. It lands somewhere else, and throws the pilot onto the ground. Hiltz is there, and he is not happy that the pilot did such a bad job since he lent him his Organoid. The guy wants another chance, but Hiltz refuses.

Later on, Krueger wants Van to be part of the Guardian Force, a special unit dedicated to protecting the peace. Van and Fiona decide to join, and they say goodbye to Van's sister. She gives him his father's knife, and they run off into the sunset in the Blade Liger.

Quotes:

"Then there's no sign of Zoid Eve here?" -Fiona
"I'm honored. What a pleasure this is to be able to come across the great hero that defeated the Death Saurer." -Hiltz
"I'm a Zoid pilot. The military is too rigid for a guy like me." -Van Freiheit.