A young boy, Ruuji Familon, is assisting his father in recovering a Zoid from the bottom of a lake when his village is attacked by silver-plated "Bio-Zoids". None of the villagers are able to pilot the excavated Zoid, until Ruuji accidentally falls into the cockpit and activates it. He names the Zoid "Murasame Liger", and, with it, is able to fight off the invaders.

A Lance Stag and Sword Wolf appear and assist Ruuji in defeating the invading Bio-Zoids and dousing the fires in the village. The Zoids' pilots introduce themselves as Re Mii and Ra Kan, and explain that the Bio-Zoids' target was the village's Generator. When the Bio-Zoids attack again, Mii and Ra Kan are incapacitated, leaving Ruuji to fight on his own.

Ruuji is about to be crushed, but Murasame Liger defends itself of its own accord. Heartened, Ruuji fights back and drives away the Bio-Zoids for good, but, during the battle, the village's Generator is damaged and shuts down. Ruuji, Mii, and Ra Kan leave the village in search of a mechanic who can repair the Generator.

The group arrives at a trade city. While Mii and Ra Kan go to scout out the area, Ruuji takes Murasame Liger into the city by himself, hoping to find a Generator mechanic. He is treated to lunch by a girl named Kotona, and while he is away from his Zoid it is stolen by a gang of thieves. Kotona reveals that she had planned all along to use the Liger as bait so she could catch the thieves. They use Kotona's bird-type Zoid, Rainbow Jerk, to catch up with the gang and recover Murasame Liger.

While Ruuji continues his search for a Generator mechanic, he runs into Kotona again. Kotona's friend Garaga has been harassing her, so she asks Ruuji to pretend to be her fiance in order to discourage him. Garaga challenges Ruuji to a Zoid battle to win Kotona's love. Ruuji fights against Garaga's Deadly Kong, but Ra Kan interrupts the battle.

Garaga is revealed to be the leader of an anti-Digald guerrilla force. When his friends come under attack by Digald Bio-Raptors, Garaga enlists the help of Ruuji and the others to defend them. The group drives off the attacking Bio-Zoids, but Mii predicts that this is only the beginning.

The Bio-Raptors mount another attack on Garaga's base. The rebels plan a trap to defeat the Digald forces, but their plan is turned against them. Kotona is able to evacuate the rebels, but Ruuji and the others are surrounded and trapped inside the hideout. Murasame Liger manages to break down the wall and the group escapes into the valley.

The group leave for the village of Sakusa to find a Zoid mechanic, who is a friend of Ron's. However, they are forced to turn back after Rainbow Jerk runs out of Reggel. The city has been taken over by Digald forces, so Ruuji sneaks in and meets up with Haara. They form a plan to take Reggel from the Generator without Digald catching them. Garaga and Ra Kan distract the Bio-Raptor guards, and Ruuji retrieves the Reggel, but he is spotted by Zairin, and the Mega-Raptor leads a counter-attack against them.

Having escaped from the Bio-Raptors, Ruuji and the others arrive at Sakusa village, and meet the mechanic who was repairing Ron's Zoid, Bamburian. Ron wants to test Bamburian in battle, and challenges Ruuji to a friendly match. Ruuji loses the battle, and becomes determined to prove himself. He fights against a wild Zoid by himself, but is overwhelmed when more wild Zoids show up and attack him. He is saved by an unknown Zaber Fang-type Zoid.

The morning after Ruuji left, he still has not returned. Kotona goes out to search for him, and comes across him staying at the home of the man in the Zaber Fang-type who saved him from the wild Zoids. Kotona recognizes the Zaber Fang as Soul Tiger, and its pilot as Seijuurou, supposedly the greatest Zoid pilot ever. Ruuji begs Seijuurou to teach him to become stronger, and he agrees to travel together with them.

The group finally has a lead as to the location of a Generator mechanic, a man named Ferde. They head off into the mountains, but Mii gets sick on the way. Ron, who knows a lot about herbs, tells Ruuji that there is a plant that can cure her, and he goes out with Seijuurou to find it.

Arriving at their destination, the group finds the city of Ze Ruft taken over by Digald soldiers. Ruuji, Kotona, and Seijuurou sneak into the city to find the Generator mechanic. Meanwhile, Ra Kan and the others are discovered and surrounded by Bio-Zoids.

The Digald soldiers in the city are taking the citizens with the ability to pilot Zoids and putting them through military training. Ruuji and the others are captured and forced to do Digald's dirty work. Outside the city, the rest of the group retreats from the attacking Bio-Zoids, and Ra Kan spots the Ze Ruft defense squad coming to take back their city.

The Ze Ruft defenders are completely overwhelmed and destroyed by Digald. Ruuji finally learns where Ferde is, and as the Ze Ruft forces mount another attack, the group goes to find him, only to discover he has been killed by Digald. The group escapes from the city empty-handed.

Ruuji is desperate to go back and help the people of Ze Ruft, but Ron disagrees. Ruuji and Garaga head back to the city on their own, and while they are away the rest of the group comes under attack by a large force of Bio-Zoids. Ruuji and Garaga rush back to help them. Everyone escapes safely, but the group is separated.

Separated from his friends, Ruuji runs into an anti-Digald group calling themselves "Tenka Muteki no Muteki-dan", and meets their leader, a woman called A Kan. The group assists Ruuji in searching for his friends and he is soon reunited with Garaga. They set a trap and attacks a Digald supply train, but Bio-Raptors arrive and Ruuji and Garaga are forced to save the Muteki-dan.

Muteki-dan intercepts another Digald supply train, but this time Digald has brought a full force of Bio-Raptors, and the Muteki-dan are completely wiped out. Garaga, in his anger, unleashes Deadly Kong's ultimate weapon, sending it into a berserk rage. It attack everyone and everything, including Murasame Liger. Ruuji calls out to Deadly Kong and it finally calms down.

Mii, Ra Kan, Seijuurou and Kotona have reunited safely at Pikuru village. The villagers discover that they are being hunted by Digald, and plan to hand them over to the Bio-Raptors to protect their village. Ruuji and Garaga return just in time to save their companions.

An army of Bio-Zoids arrive at Pikuru village, led by Georg, who is determined to defeat Ra Kan. When they discovers that the group has already left, the Bio-Zoids begin burning down the village. Ruuji spots the smoke and convinces the group to head back and help the villagers. Ra Kan faces off against Georg, but with his injured arm he is unable to pilot Sword Wolf properly and is about to be defeated. Enraged, Ruuji attacks Georg, and Murasame Liger transforms into a Hayate Liger for the first time.

Georg's Bio-Tricera is defeated and Murasame Liger reverts to its old form. Ruuji names the new form "Hayate Liger". The next day, while the group is helping to repair the village, Ruuji thinks about Digald's continued attacks, and wants the group to form an organized resistance against them, with Ra Kan as its leader. Ra Kan tells the story of the kingdom he once ruled and how it was taken over by Digald. To test Ruuji's determination, Ra Kan challenges him to a fight, and quickly overpowers him. Just as the battle ends, Ron finally catches up and is reunited with the group. Ra Kan makes the decision that the group will return to Mirodo village.

Ruuji, Kotona and Ra Kan head back to Mirodo village in Rainbow Jerk. They pass by a city under attack by Digald, and Rainbow Jerk is attacked by a Bio-Ptera, a flying Bio-Zoid. They manage to escape, but arrive at Mirodo to find the village slowly dying. Ra Kan and Ruuji explain the situation to the villagers and they agree that they should fight Digald. Ruuji and the others head back to rejoin the rest of the group.

The group arrives in Zuuri City, and learn about Mii's past and the death of her parents. Ra Kan is reinstated as ruler of the city, and promises to the citizens that he will defeat Digald and bring peace back to the world. Seijuurou gives Ruuji some new training to help him pilot Hayate Liger.

The group splits up to send appeals from Ra Kan to several resistance groups, asking them to help in the coming battles against Digald. Ruuji is the last to leave, but not before getting some more training in with Seijuurou. On the way to his destination, he is attacked by Bio-Zoids, and Murasame Liger transforms into Hayate Liger to fight them off. The rebels agree to fight with Ra Kan, and they return to Zuuri City with Ruuji.

Zairin thinks back to the time his village was destroyed by Bio-Zoids, how he came to be a Digald Bio-Raptor pilot himself, and how General Jiin told him of his goals to become a god and control the entire Digald Empire. Jiin later promoted Zairin to the rank of Major and gave control of Mega-Raptor to him. Meanwhile, in Zuuri City, the rebel troops gather and prepare for battle. The first Bio-Zoids attack and are defeated with the help of Ruuji and Hayate Liger.

The war against Digald begins, with Ra Kan's rebel army heading to its first target, Torafu. However, Zairin is able to read the army's movements and anticipates the attack. Seijuurou heads to Atakka as a distraction, while the rest of the rebels head down the River of Fog to Torafu.