The story opens with a young man named Kid Zone inhabiting an area called Motley Island. Kid Zone decides that since it’s the anniversary of when he “woke up,” he should celebrate with a feast with the best delicacies on the island. He’s able to fend off the hostile magic-powered endemic life of the island with magical abilities of his own, such as his ability to manifest a halberd which he shows great proficiency in wielding, and his ability to emit and command pure energy.

Going throughout the regions of the island, he collects a puzzle fruit from Emerald Bluffs, a platter clam from Sapphire Coast, some primordial sirloin from Ruby Valley, some whispering sprouts from Topaz Jungle, and some strata chocolate from Obsidian Cavern. As he sits down to give thanks and eat, the whole island is rocked by a great impact. He follows the smoke to Diamond Mountain in the exact center of the island. On the path to the summit, he trades blows with some strange characters, not quite being but not quite beast. At the summit, he’s surprised to discover a massive craft lodged into the mountain where a slightly less massive mechanical construct is doing battle with an old man on a flying surfboard-like craft. The old man is knocked off the board and Kid Zone accidentally steps on it. The board seems to react to him and somehow he’s sent flying into the sky where he disappears in a flash of light.

Act 2

Kid Zone ends up landing in the intricately mechanical Tinker Castle, where he’s shocked to discover other intelligent beings, and even more shocked to discover that he can communicate with them despite never encountering things like them before. He’s drawn to a ruckus where he sees another young man doing battle with similar strange characters with what looks like a top and the ability to command energy in motion.

Spinner introduces himself as a Guardian and welcomes Kid Zone as his kin. Kid Zone doesn’t understand what a Guardian is, which Spinner replies that he doesn’t quite understand either. All he knows is that he woke up one day in Tinker Castle and the people recognized him as a Guardian, their ancient protectors, from his abilities. He says that the characters they defeated are called Hollows, and they’re the forces of a really strange character called the Emperor.

Kid Zone discovers that he has the ability to summon the surfboard-like construct the same way he summons his halberd. The people of Tinker Castle refer to it as a Speeder, the vehicles that the Guardians would use to travel between Zones. After defeating the Emperor’s commanding Greater Hollow, the Speeder reacts and Kid Zone, accompanied by Spinner, boards it to the next Zone.

Act 3

They end up in Heavenly Babylon, where for no apparent reason, they are attacked by another Guardian called Stalwart, who wields a claymore and commands natural forces. Stalwart demands that they leave, and does not accept the fact that they don’t know how. As they traverse Heavenly Babylon, they are occasionally ambushed by Stalwart, who sometimes even uses mechanical traps in an attempt to smite them. Eventually, they corner Stalwart in a gladiatorial arena, where Kid Zone comes out on top.

Suddenly, a siren goes off and Stalwart attempts to rush off to answer it, but appears too weak from the intense battle. Kid Zone and Spinner carry him to where he indicates and find a marvelous multi-faceted clear crystal being beset by Hollows. Kid Zone and Spinner attempt to fight them off, but a Greater Hollow shows up and smashes the crystal. After seeing this, Stalwart’s rage overcomes his fatigue and he smashes the greater Hollow.

Stalwart says that the artifact was called the Power Prism, an incomparable treasure that his ancestors, a specialized line of Guardians, have been safeguarding in solitude for many generations. He remarks that the Power Prism has a failsafe which scatters 300 shards across neighboring Zones, and demands that Kid Zone and Spinner help him find them. The Speeder fires up once more and Stalwart hops along.

Act 4

Their next stop is Mystic Plateaus. When Kid Zone attempts to touch down, he gets run down by a strange young woman. Their eyes meet for a moment, then she gets up and starts running, telling the others to do the same. Suddenly, they are beset by an oncoming horde of Hollows. After defeating their adversaries, they decide to chase down the first being they made contact with.

They meet her and she introduces herself as Bloomy, a Guardian. She tells them that she was trying to lure the Hollows away from a special place. Like Kid Zone and Spinner, she woke up in her Zone with no memory of how she got there, where she came from, or how long she’s been there. However, she does remember someone telling her about the special place, and that it’s her job to protect it and guide other Guardians to it one day. Now that she’s encountered other Guardians, she feels that she must guide them to the special place.

They traverse the mesmerizing terrain, defeating many Hollows in their path, until they come upon a dome containing numerous inscriptions and pictures. However, they realize they’ve been followed by a Greater Hollow, who sets numerous bombs throughout the structure. Bloomy finally displays her abilities as a Guardian with a deck of cards she is able to control the size and properties of, along with her ability to alter her environment and control things within her environment. After defeating the greater hollow and disabling it’s bombs, they’re finally able to get a good look at the inscriptions. They don’t understand a lot, but they see seven prominent symbols. Stalwart is able to recognize that the inscriptions are written in the same language as the ones all over Heavenly Babylon, and is able to recognize a symbol representing the Power Prism. Unfortunately, he says he was never taught how to read the language. The Speeder reappears and they all board it to the next Zone.

Act 5

Touching down at glamorous Neon City, they are caught between a pursuit of police chasing a woman with the abilities of a Guardian, who has stolen a small fortune in valuable objects called Chips. They pursue her throughout the city, and must rectify the mischief she causes in order to stop them and other authorities. As they follow her, they notice that she is making her way downward from the aristocratic sections of the city into the slums. Eventually, they confront her at an abandoned industrial park, where she displays her mastery of twin pistols and ability to command mystic ether. Eventually, they weaken her to where she can no longer resist, but before they can deliver the final blow, the residents of the slums interfere en masse. However, she begs them to stop and offers to surrender in exchange for their safety. She reveals her name as Sylene and that she was born in the slums, who were constantly neglected to give more to the aristocrats of the city. Guardians used to offer much-needed humanitarian aid, but over time they disappeared. One day, when facing a moment of extreme emotional significance in her life, she found that she had inherited the powers of a Guardian and vowed to use them to help her people, even if it meant committing acts of heresy against the Guardian code. She reveals that Chips are a form of raw matter that can be used to build all kinds of necessities and luxuries, which the slums need to maintain their livelihoods.

Before they can make a decision, the Hollows attack, this time led by the Emperor himself. He demolishes most of the slums in an attempt to build a garrison on top of it. Kid Zone and his friends rush to their aid, and the Emperor is surprised to see a new generation of Guardians, as he had believed he had killed them all. The Guardians smite his forces and defeat his war mech, he retreats, but ominously states that once he obtains the “Seven Miracles” no number of Guardians will be able to stop him. Sylene offers to accompany Kid Zone and his friends, even flirting with each of them. The Speeder reappears, and somehow splits into five extra ones. Led by Kid Zone, they all disappear into the sky.

Act 6

Kid Zone is surprised to discover that they’d circled back to Motley Island, and even more so to discover that it’s layout is completely changed and infested with Hollows. They traverse a path through Emerald Bluffs, Sapphire Coast, Ruby Valley, Topaz Jungle, and Obsidian Cavern, defeating a Greater Hollow at each one. Eventually, they make their way to the fortress built on top of Diamond Mountain, where The Emperor is surprised to see them as he had claimed the island as his new secret base. They defeat the War Mech and chase the Emperor back off the island, and deep within the fortress they find the old man.

The Old Man reveals himself as Bontal, the last of the Guardian Council of Elders. He states that the Emperor appeared out of the abyss between Zones and launched an all-out surprise attack against the Guardians, leaving no prisoners. He states that the Emperor has a mysterious ability to disassemble and reassemble matter however he likes, and is able to do so to magic-saturated matter to create hollows. He appears to have no tolerance to the magical and chaotic Zones and seeks to bring his brand of order onto them, sometimes even by destroying them. Bontal stated that he foresaw the previous generation of Guardians would be inadequate to defeat the Emperor, so he took the children of several prominent Guardians, altered their memories, and sent them out into the Tree of Life in the hopes that they would grow up to oppose the Emperor. He states that there are two ways to become a Guardian: Either accept and learn to control one’s emotions, or be born to Guardian parents.

Finally, Bontal reveals the Emperor’s ultimate goal: to gain control of the Seven Radiances: Sources of unparalleled magical energy that, once assembled, can grant unlimited power. He then states that he recognizes Stalwart’s bloodline and reveals that the Emperor destroyed the Power Prism because it possesses the ability to command any form or quantity of magic, making it the only thing able to neutralize the Radiances’ power, or increase them to whole new levels.

They travel back to Mystic Plateaus after being taught to read the secret language of the Guardians by Bontal and discover that the Seven Radiances will appear during times of great significance, and will be guarded behind Doors of Darkness to create trials so that only the worthy will be able to obtain them.

Act 7

It is at this point where the story diverges into multiple routes for multiple endings.

In the first ending, where they ignore the Radiances and simply destroy the Emperor’s war mechs in every Zone: The way opens to the No Zone, the Emperor's main base. There they face off with tricks and treachery uncounted until they reach the Emperor, who decides to take matters into his own hands. When they appear to have defeated him, it's revealed that his body is merely a shell manipulated by a core of pure energy that disassembles everything in range and reforms it into a super war mech. After they defeat it, the Emperor is sent back into the void from whence he came. Our heroes celebrate and are celebrated, but the Emperor is revealed to have spent their downtime building an even bigger army than ever before and planning a new attack.

In the second ending, where they find all of the Radiances, Kid Zone undergoes a transformation into a being of night-unlimited power called the Ultimate Guardian to kick the Emperor's mega war mech's keister to atoms. Later, the Emperor is revealed to be alive in the furthest depths of space, swearing revenge regardless of how many eons it would take to achieve.

In the third ending, where they gather both the Radiances and reassemble the Power Prism: The Prism appears before them in their hour of need and amplifies the Radiances' power to unimaginable levels, which allows them all to merge into the Perfect Guardian that defeats the Emperor's Omega Mech and erases the Emperor from existence. In the aftermath, Bontal is uneasy as he reveals he had a revelation about the Emperor's true nature at the moment of his destruction. The Emperor was a manifestation of the force of entropy, and now that he was gone, something new and possibly much worse would emerge to take his place.

In the fourth ending, where they do all of the above and gather Chips from all over to rebuild the slums into the envy of all civilized Zones: They end up creating a containment unit that can trap cosmic entities and their power forever, which they do to the Emperor after defeating him.