Prior to the series there was war between the Guylos Empire and the Helic Republic which ended in a ceasefire. Not much is stated about the war other than that Van's father fought and died in it. The series starts with Van being chased by a group of bandit Zoid pilots and ends discovering the organoid Zeke in some ruins. Zeke revives an abandoned Shield Liger, which Van uses to fight off the bandits. After that, he discovers Fiona in the ruins that he found Zeke in, and finds that she has no memory of who she is. When Van returns to his village, the gang bandits return and try to take Zeke from Van. To keep his village safe from them, he leaves with Fiona. During that time in some more ruins Van hears Fiona speak of something called Zoid Eve and decides to help her find it in hopes that it help her get her memory back. Shortly afterwards, he meets Irvine. Initially, Van and Irvine are enemies because of Irvine's desire to take Zeke, but end up traveling together when they meet with traveler Moonbay, and Van ends having to stay with Moonbay because she blew up her cargo to help him.
Later, the four end up at one the Republic's army bases, and end up having to help stop an invasion by the Empire orchestrated by Prozen. After that, Van, Fiona, Irvine and Moonbay preferred to stay out of the war. However, Van ends up getting involved somewhat when he meets the Guylos ace pilot Raven, whom he quickly holds a grudge against after seeing Raven's brutal nature, but proves no match for him their first battle. Van later challenges Raven again, loses, and Zeke suffers near-fatal damage, but Van manages to save him. During this time the Imperial army is marching farther and farther in Republican territory but are eventually stopped by the Republic's Gojulas. Van and the others eventually reach the Republic's capital in hopes of finding information about Zoid Eve, but only end up getting caught up in the Empire's assault on the city. During the battle Van is finally able to defeat Raven.
The war is stopped when the Empire's crown prince Rudolph orders a ceasefire, but Prozen refuses to give up on conquering the Republic, and so attempts to assassinate the prince, but his attempt is foiled by the bandits Rosso and Viola who kidnap the prince in attempt to gain money. During this time, Prozen finds the remainants of legends about the Death Saurer, attempts to clone it, and also creates the Geno Saurer for Raven to use. Raven uses the Geno Saurer to destroy Van's Shield Liger, but was unaware that Zeke and Fiona revived the Shield Liger as the Blade Liger. During this time it's revealed that Fiona is actually an ancient Zoidian that existed before humans came to the planet Zi. Rudolf joins Van and his friends who try to take him to the Empire's capital Guygalos to stop Prozen from taking over the Empire and restarting the war. During this time, parts of Imperial army loyal to Prozen and some that were manipulated into fighting them try to stop them. Eventually, Van faces Raven again and after an extremely difficult battle destroys the Geno Saurer. He does this by using one of the Blade Liger's blades(the other was snapped off during the battle) along with his shield which disperses the charged particles. However, Raven survives thanks to his organoid Shadow. Although Rudolph is returned to the capital, Prozen attempts to use the cloned Death Saurer to take control, which goes on a rampage and almost destroys the capital and joint forces the Empire and Republic that are powerless to stop it, but Van is able to destroy the Death Saurer using the same technique used before with Raven's Genosaurer and appears to kill Prozen in the process. Rudolph is then crowned the emperor and peace finally starts to settle between the Empire and Republic, but Van and Fiona don't take part in celebration and instead leave to find Zoid Eve.
Two years after the Death Saurer's defeat, Van is shown to be part of the Helic army. On a trip home he meets up with Fiona, and the two decide to try to find the Zoid Eve again. Over the course of their adventure, the two meet up with old friends, along with new ones. Old rivals reappear, new rivals emerge, and there is a plot to restore Zoidians to power, even though all humans have to die for it.

Van Flyheight

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Van Flyheight is a teenage orphan of the previous war between the Republic and Empire. His home is Wind Colony Village, just within the borders of the Helic Republic. Van has an older sister, Maria, who is in her late teens. Their father, Major Dan Flyheight, was a pilot with the Republican Army, using a Command Wolf called Zeke. He was killed defending the Wind Colony from an Imperial attack when Van was five. At the start of the series, Van is chased into series of ruins by a trio of trigger happy bandits. He then finds two capsules in the ruin. Van opens one to find an Organoid, whom he names Zeke. He then fights off bandits in a Shield Liger, which was brought back to life by Zeke. Van then opens up the second capsule, and finds a girl, who he names Fiona. Van then starts a journey to find Fiona memories, and becomes caught up in a new war, and a plot to take over Zi. Van is a bit dense to start with, but is loyal to his companions and has a good heart. His open nature means that many people are attracted to him, and he enjoys a good challenge. He pilots a Shield Liger, a lion type Zoid that can deploy a shield in front of itself. It later evolves into a Blade Liger, which gives it a pair of laser-edged blades capable of cutting through all but the densest of enemy armor. His favorite food is mentioned as papaya.

Voiced by: Daisuke Kishio (Japanese), Matthew Erikson (English)

Fiona

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Fiona is young girl awakened from stasis by Van. She suffers from severe amnesia, and is unable to remember anything. Van gives her the name "Fiona", and the two set off to discover who she is. As her memories return, it is learned that Fiona is actually Elisia Linette, one of the last members of the Ancient Zoidian race. Her driving goal is to discover something known as the 'Zoid Eve', supposedly the source of all Zoids' power. Although a bit naive at first (going up to bandits and demanding they release her friends), she matures over time and eventually serves as Dr. D's brilliant assistant. While she and Van had somewhat of a rocky start, the two would grow close, and form a bond. It is hinted that Fiona and Van did develop romantic feelings for one another, as Fiona did give Van a kiss during his last battle with Raven. Later in the series, Irvine even pointed out Fiona's love for Van.

Voiced by: Makiko Ohmoto (Japanese), Carol-Anne Day (English)

Zeke

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Zeke is an Organoid dinosaur, a small Zoid imbued with many powers. Awakened by Van, Zeke is named after the Command Wolf piloted by Van's father. Zeke's primary ability is to fuse himself with another Zoid, increasing its combat potential dramatically. Zeke is able to use this ability to resurrect destroyed Zoids, and to evolve Zoids into more powerful forms.

Voiced by: Takuma Suzuki (Japanese), Dave Pettitt (English)

Irvine

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Irvine is an eighteen-year-old mercenary, and the "tough guy" of the series. Initially interested in capturing Zeke, he later joins Van and Fiona after losing this desire. Although cold-hearted in appearance, Irvine shows a soft side on more than one occasion. He is a skilled pilot, who uses a modified Command Wolf with a powerful long-range beam cannon. When his Command Wolf is severely damaged, its combat data is transferred to an experimental Zoid, the Lightning Saix, which uses extreme speed to overwhelm the opponent. While he wears an eye patch, he has full function of both his eyes, and uses the eye patch as a camera.

Voiced by: Keiji Fujiwara (Japanese), Mark Gatha (English)

Moonbay

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Moonbay is a trader, who often smuggles weapons using the Gustav, an armored insect Zoid capable of pulling 250 tons of cargo. She is considered to be a free-spirited individual, who is not afraid to speak her mind. Although appearing greedy and selfish, Moonbay is a good person. She does like to sing, although she rarely stays on key.

Voiced by: Kumiko Watanabe (Japanese), Onalea Gilbertson (English)

Raven

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Raven is the top pilot of the Guylos Empire, adopted by Prozen after his parents, Zoid researchers, were killed by the organoid Ambient. He is selected for his prodigious piloting abilities, which are complemented by the Organoid, Shadow. Raven is extremely anti-social and reserved, and holds a deep dislike of all Zoids. He considers Van to be his rival, and swears not to rest until Van has been killed by his hand. Raven pilots a Zaber Fang, which is destroyed in a battle with Van. He then pilots a Genosaurer which is destroyed by Van in another battle. It is replaced by a prototype Genosaurer, which later evolves into the powerful Geno Breaker.

Voiced by: Mitsuki Saiga (Japanese), Scott Hendrickson (English)

Gunther Prozen

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Gunther Prozen is the main villain of the series. He is the Regent of the Guylos Empire, an Admiral in the Guylos military, and the second in line for the throne of Guylos. Prozen arranges for Prince Rudolph, next in line for the throne, to be kidnapped and assassinated so that he can seize power after Emperor Zeppelin's suspicious death. He plans to use the Deathsaurer to take total control of the world. He is believed to be killed after his Death Saurer is destroyed, but is shown to have survived as the Dark Kaiser.

Voiced by: Houchu Ohtsuka (Japanese), Dave Kelly (English)

Hiltz

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Hiltz is an ancient Zoidian with a red organoid named Ambient. His driving goal is to restore Zoidians to power, even if all humans have to die to do so. He pilots the Death Stinger and later merges with the Ultimate Death Saurer. Hiltz is the main antagonist of Zoids Guardian Force, and arguably the entire series as his arc is tied to Fiona's past and the quest for the Zoid Eve. He is killed in the final episode when Van is fired through the gravity cannon and penetrates the Ultimate Death Saurer.
Voiced by: Takahiro Sakurai (Japanese), Scott Roberts (English)

Reese

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Reese is an ancient Zoidian with a blue organoid named Specula. She pilots a Double Sworder, and later upgrades to an advanced Genosaurer which was developed based on the data of Raven's Geno Breaker. She and her organoid both possess psychic abilities, and she often uses psychological warfare and mind-control to disable her enemies. While she is first an ally of Hiltz, she changes sides after she finds out Hiltz has been using her all along. She appears to have some feelings for Raven, as she does help him come to terms with his past.

Voiced by: Noriko Hidaka (Japanese), Mariette Sluyter (English)

Doctor D.

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Doctor D. is a self-confessed mad scientist once employed by the Republican Army as a Zoid researcher. He is considered Zi's foremost expert on anything Zoid or Organoid related, and enjoys hanging around with Van and his group. His attitude and demeanor irritate Van, but Doctor D.'s knowledge comes in handy on several occasions. Voiced by: Dave Pettitt
Prince Rudolph Zeppelin III is the grandchild of Emperor Zeppelin. Rudolph is placed into the care of Van by Rosso and Viola, former waste gangers. Van agrees to help return Rudolph to the Guylos Empire capital, Guygalos, and to teach the boy how to pilot a Zoid properly. Although Rudolph's identity is initially kept hidden from Van and his friends, Doctor D. soon reveals the truth about the Crown Prince. Rudolph is an eager, friendly person, who wishes to be able to emulate Van in piloting skill. Rudolph is quite naive and prefers reasoning over fighting, even with Raven and Prozen. He also deeply cares for the Guylos empire and hates seeing others around him hurt.

Voiced by: Tomoko Ishimura (Japanese), Elinor Holt (English)

Karl Lichen Schubaltz

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Karl Lichen Schubaltz is one of the Guylos Empire's greatest Zoid pilots. Schubaltz is an honorable fighter, and wishes to see peace between the Republic and Empire as opposed to total destruction of both sides. He has a younger brother, Thomas, who doesn't appear until Guardian Force. He both loathes and distrusts Prozen, though he doesn't do anything to stop him. Initially a major, he is later promoted to the rank of colonel. Karl Schubaltz pilots the Dark Horn and the Iron Kong, as well as a custom Saber Tiger.

Voiced by: Yuji Ueda (Japanese), Jonathan Love (English)

Thomas Richarf Schubaltz

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Thomas Richard Schubaltz is the younger brother of Karl Schubaltz, and pilot of the Dibison. He excels at technical tasks, and is the creator of the BEEK AI unit, which can be installed into a Zoid, and communicates through a series of beeps. When he first meets Fiona, he falls in love with her. This serves somewhat of a gag, as Thomas is shown to compete with Van for Fiona's feelings (though neither Fiona or Van know about this).

Voiced by: Kentarou Itou (Japanese), Ryan Luhning (English)

Rob Herman

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Rob Herman is the commander-in-chief of the Red River Unit at the Red River base bordering Imperial territory. He is also the son of both the Republic's former and current Presidents, but he is a confident soldier who does not appear to rely on the influence of his family in order to benefit himself. Instead, he prefers to perform his duties and to earn his rank in the army on his own. In fact, it is to be noted that in one of the episodes, it is hinted that he is so detached from his familial ties that he has not called his mother, the current President of the Republic, "Mom" in several years, instead addressing her by her proper title as any other soldier would. The Zoids he has been seen piloting most often are a Pteras and a Gordos. He has also been seen piloting a Gojulas and a Shield Liger from time to time.

Voiced by: Jin Horikawa (Japanese), Kurtis Sanheim (English)

O'Connell

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O'Connell is the second-in-command to Rob Herman, and most commonly pilots a Command Wolf and Pteras. His loyalty is a notable character trait, as he appears quite upset when Herman is missing in action, leading him to accept the assistance of Van, Moonbay, Irvine and Fiona (for a price).

Voiced by: C. Adam Leigh