Helmut has been arrested by the Peacekeepers for sabotaging the Gojulas Giga. RD goes to the PKB's HQ and demands to speak with Helmut, but is thrown out. He meets up with the rest of Mach Storm. Hop tells him that Gummie has been demoted to traffic duties. Furthermore, Ciao and Deed have been reassigned to desk jobs and are also being questioned.
As they watch, a fleet of Gustavs take away the PKB's Goreheks and Arosaurers. Hop explains that the PKB are replacing them with the new Chimeras. Hop adds that the Zoids will likely be scrapped.
Inside PKB HQ, Helmut is met by a mysterious man in sunglasses, similar to those worn by the Cryptic group. Helmut recongises him as Marvis! Marvis informs Helmut that he's the new chief of the PKB, and the new mayor got him the job. Helmut tells Marvis that he was set up, Marvis admits this, but says that all the evidence is against him, and that Helmut doesn't stand a chance.
RD and Sweet return to Mach storm, only to find that the team has been ordered to shut down pending an investigation. They watch as Amy, Sigma, Hop and Matt are lead away by the cops. RD is about to charge in, when Vareth appears, and warns him against it.
Alpha appears on the TV, introduced as the new mayor. Vareth explains that he's behind the attacks, and that he's trying to remove all opposition. He's even detaining all the other Zoid fighters. We see PKB troops arresting Rastani, Rattle, Malloy and other Z-Fighters.
Alpha addresses a crowd, vowing to rebuild Blue City, making it the greatest city on Zi, and asking for their support. He promises to make the city safer by rounding up and disposing of all the Zi-Fighter Zoids. A monitor shows a group of Zoids lined up (A green Gorheks, Dark Spiner, blue Leoblaze, blue Helcat and white Blade Liger). A Squad of Storm Bros. open fire on the Zoids. RD, angered by this, runs off, vowing to stop Alpha.
Sandra speaks to Dr Pierce. He reveals that he was behind the Gojulas Giga's sabotage, and that he's also out to destroy Mach Storm. Sandra warns him that he's playing a dangerous game, but he says that he knows exactly what he's doing. He says that he has been compiling data about every battle, every Zoid and every Z-Fighter. Sandra asks him if he was working for Alpha, but he doesn't reply.
At the Arena, the Storms have destroyed most of the Zpids and are about to destroy the Dark Spiner, when RD interrupts them. He tells Alpha to stop now. In response, he sets the Storm Bros. on RD.
Gummie's Giga is being taken away, when he finds out that RD is attacking the Mayor. He activates it, and attacks the PKB forces, destroying a horde of Storm Bros. He threatens Alpha, and ask him who's behind all this. Rebecca (Alpha's assistant, presumably the same Rebecca who was piloting the Dimetroptera) moves to protect him, but he tells her not to worry. Instead, the ground cracks open and the black Seismosaur appears!
The Seismosaur opens fire, disabling the Giga. RD says that he'll help out, but Gummie tells him to go and help Helmut, and that he'll handle the Seismosaur on his own. RD leaves, but finds that his path is being blacked by a horde of Storm Zoids. Before they can attack him, however, they are destroyed by a massive energy blast. RD looks up and sees the Energy Liger. The Energy Liger leaves. RD continues, all the while being watched by a Gorilla Tron. Back at the arena, we the Seismosaur stands over the defeated Giga.
At Savage Hammer HQ, Sandra speaks to Alpha, who is celebrating. He warns her that she is nothing without him and his father. As his adopted sister, she got where she is today, including forming Savage Hammer, through him. He tells her that he was able to use her need for revenge on Helmut as a cover for all his operations. He also thanks Burton for all his help, reveling that he was working for him all along.
Gummie is thrown in prison with the rest of Mach Storm. Meanwhile, RD and Sweet are hiding out at Haldo's hanger. He advises them that they're safe here for the moment. RD, however, is upset about what has happened, and vows to stop Alpha.
Sandra calls up all her contacts, but they all say that they can't do business with her and cut her off. Agry, she warns Alpha that he can't mess with her. Blake enters, and Sandra asks why he's still here; she's just disbanded Savage Hammer. She also tells him about what happened the first time that he and RD battled. Blake's Zoid malfunctioned; Sandra told him that RD was behind it, but in fact it was her. She wanted him as a part of her team. Getting all teary, she tells Blake that he must hate her for it. He says that he doesn't, and has other work to do, while staring out at the PKB headquarters…