Some Guysack sleeper Zoids are activated by a huge flying Zoid, the Whale King. Then some Hel Digunners chase a Rev Raptor sleeper, and capture it. They are confronted by Thomas, but a black Command Wolf (guess who?) attacks him and damages his Dibison. Thomas then sees the Whale King fly up into the sky. Inside the Whale King, Van gets out of the Rev Raptor that was just captured. He activates a signal for Fiona and Zeke to track the Whale King in the Liger. Van walks around for a while but then he's spotted. He runs, but then finds a guy with an eye patch (guess who?), who punches him out.

Fiona and Zeke track Van's signal and find Thomas. Their mission is to find out why the sleeper Zoids are being captured. Meanwhile, Van is locked in a room and the guy with the eye patch, Irvine, comes to talk with him. Irvine is after some reward money, and Van wants to know what's happening to the Zoids. The Whale King lands at a base, and then has to wait for a sandstorm finish. Van and Irvine make it look like Van's escaped in a truck and Irvine shoots the truck. A guy wonders about Irvine and goes to check him out on a computer. Later, Irvine meets up with Van, who is still there, and they go into the underground base. Irvine says that he was hired by a rich guy to find his stolen Zoids. He also suspects that there's something bigger behind all of this.

Irvine and Van find a huge pile of Zoid remains, and Van notices that the cores are gone. Then the both of them are captured, and Irvine finds out that Van is in the Guardian Force. They see what's happening to the Zoid cores. They are being genetically altered in an attempt to make a more powerful Zoid. Van and Irvine think that it's disgusting, and then the Whale King is attacked by the Blade Liger and Dibison.

Zeke flies into the Whale King and rescues Van and Irvine. Thomas and Irvine, who gets into his Command Wolf, and fight some Hel Diguners that come to defend the Whale King. Van takes Fiona to the Whale King so she can free all of the sleeper Zoids that were captured, and then he goes to help Irvine and Thomas. The Hel Digunners are beaten and Fiona sets the last sleeper Zoid free. The Whale King takes off and Van runs to save Fiona. He jumps up and grabs onto it with his claws, but the Liger starts to slip. Van tells Zeke to take over and gets out of his Zoid and manages to get into the Whale King. A guy attacks Van, but then some engines start exploding and the guy is thrown out of the Whale King. Hiltz appears and says that he's responsible for the explosions, and that he's just tying up some loose ends. Then he leaves with Ambient.

Irvine saves Van and Fiona using a Pteras and the Whale King crashes. Later, Irvine says that he doesn't want to join the Guardian Force, but it was nice seeing his old friends again. Then he runs off into the sunset with his Command Wolf.

Quotes:

"It's my business. I've been looking for these guys, and more importantly, I've been looking for these Zoids." -Van Freiheit
"At first I was only interested in the reward, but after looking around, I began to think that there was something much bigger behind all of this." -Irvine
"Think I'd let you steal the show? Thomas Schubaltz to the rescue!" -Thomas Schubaltz, duh
"You and this ship are both going down. Just tying up loose ends." -Hiltz