Cole has been caught in the dangerous magical land of the Outskirts for several months. Fortunately he’s been able to find and rescue Dalton, his best friend from Earth. Cole travels with Dalton and another friend, Jace, as they aid young princess Mira in her quest to find and help her four sisters, gifted young women who have had their magical powers stolen by their father, the evil High Shaper. He is the ruler of the Five Kingdoms of the Outskirts.
Mira is bound for Zeropolis, a technologically advanced city-state where her sister Constance is hiding. They are on the run from Enforcers sent by the High Shaper, including the most dangerous Enforcer, the Hunter. Their adult guardian is Joe, a member of the revolutionary group known as the Unseen. This group supports Mira and her sisters and wants to overthrow the High Shaper.
After a skirmish with Enforcers, Cole and his friends reach the borders of Zeropolis. Hina, a servant of Trillian the torivor, a magic being from another dimension, tells Cole that Trillian believes Cole is essential to the Outskirts’ survival. Cole has shown brief flashes of magical ability in the past, and Hina says that the rules governing magic in the Outskirts don’t apply to him.
Cole and his friends continue into Zeropolis’ Post 121, a settlement outside the main city. Joe explains that harmonic crystals power Zeropolis’ technology. As they enter post Post 121, they are given new IDs and new clothes to blend in with their surroundings.
The police quickly capture Joe. They suspect his involvement with the Unseen. He sends the four kids to a gaming arcade called Axis. Once they reach Axis, they’re supposed to find the Crystal Keepers, a group of young gamers who aid the Unseen.
Cole and Jace are separated from their friends and meet a Crystal Keeper girl named Roulette at Axis. Mira and Dalton soon join them. They have to flee to the Crystal Keepers’ main base. They meet one of the Unseen’s leaders, an older man named Googol.
To avoid being arrested, most of the Unseen are hiding in the ancient, criminal-filled city of Old Zeropolis. Googol says their first goal must be to rescue Joe from Abram Trench, the Grand Shaper of Zeropolis. Trench serves Mira’s father, the High Shaper. If he interrogates Joe, Mira will be found out and returned to her father.
Trench's City Patrol attacks the Unseen base, but Cole and his friends escape. They meet new members of the Unseen, who create new IDs for them. Cole manages to access the internet and send an email to his family on Earth, although he knows that the magical laws governing the Outskirts have caused his family to forget that he ever existed. When a person arrives in the Outskirts, every memory of their life on Earth vanishes.
In order to rescue Joe, Cole receives training in how to use an advanced battlesuit and a hoverboard. Cole sprays nonlethal freeze foam at members of the City Patrol. Roulette rescues Joe, but Enforcers from the High Shaper suddenly arrive on the scene.
Cole flees, but is caught by a drone robot controlled by the Hunter. Sidekick, a robot, frees Cole, and they both proceed toward Old Zeropolis. They discover that the Unseen base in Old Zeropolis has been completely destroyed, proof that the High Shaper knows Mira is hiding with the Unseen and is encouraging Trench’s City Patrol to find her at any cost.
Sidekick tells Cole that in order to locate Mira and their other friends, he should contact Datapoint, an acquaintance of the Unseen who lives near Sector 20 in Old Zeropolis. Sector 20 is a sealed-off district because it is home to a dangerous artificial intelligence named Aeronomatron, who once ruled Old Zeropolis. Datapoint agrees to help Cole and Sidekick, and she also reveals that Blake, one of the enslaved kids from Cole’s hometown on Earth, is staying in Zeropolis as her servant.
Blake has a magical talent for creating energy crystals, particularly communication crystals that can be used to listen in on people’s private communications. Unfortunately, before Datapoint found Blake, he was working for the City Patrol as their slave, which means that Blake’s ability is partially to blame for the recent crackdown on the Unseen. Blake says that Datapoint can’t be trusted, and he makes a crystal key for Cole to get into Datapoint’s situation room and use her computer to locate his friends.
Unfortunately, Datapoint’s secret computer is actually Aeronomatron. Aero convinces Cole that he has changed his old ways and is no longer dangerous. Aero says that Googol and the rest of the Unseen are in a place called Rainday Base. Cole, Blake and Sidekick travel there and rejoin their friends.
At Rainday, they meet the Unseen’s leader, Nova, who asks for Cole’s help in finding Mira’s sister Constance. The only person who knows Constance’s location is Mira’s mother, Queen Harmony, who still lives with the High Shaper in Junction City. Cole volunteers for the mission. He dresses as an errand boy and rides a monorail train from Zeropolis to Junction City.
He infiltrates the First Castle and finds Queen Harmony. When they are alone, Queen Harmony tells Cole that Constance is Trench’s captive in Zeropolis. She says that the High Shaper is losing power and is in danger from his right-hand man, Owandell, a man who can alter the nature of magic through the use of a skill called shapecraft.
Owandell helped the High Shaper steal his daughters’ magical abilities. Now that two of the five princesses have regained their powers, Queen Harmony doubts that the High Shaper is more powerful than Owandell any longer. Queen Harmony asks Cole to secretly attend a meeting of Owandell’s spies and shapecrafters to learn about his plans.
At the meeting, Owandell talks about the Founding Stone, a piece of the First Castle, which is actually the first piece of the Outskirts. He has the stone. The Outskirts is a created world, and Owandell says that a powerful being named Nazeem is returning to the Outskirts from his hiding place in the Fallen Temple in Necronum. Nazeem appears to his followers as an image in a magical fire above the Founding Stone.
Owandell recognizes Cole as a spy. Cole wants to run away, but he finds himself drawn by the strong magic emanating from the Founding Stone. When Cole touches the stone, time stops, and he finds that he can sense magic in all the shapecrafters at the meeting, as well as sensing his own dormant magic, which had been damaged by a vengeful monster he met during his adventures in Elloweer with Mira.
He also finds that he can project his consciousness, so he communicates telepathically with Queen Harmony, who encourages him to try to use his new power to teleport away from Owandell’s meeting. When Cole unsuccessfully tries to teleport, he sees a vision of Dandalus, who says he is one of the original architects of the Outskirts. Dandalus mentions that shapecraft could destroy the entire world. Then he helps Cole by teleporting him to Queen Harmony and safety.
Queen Harmony mentions that Jenna, Cole’s friend and longtime crush, is currently in the Temple of the Still Water in Necronum. She sends Cole off on a train to Zeropolis to rescue Constance from Trench’s secret lair. Cole is arrested upon arrival and delivered to the Hunter, who turns out to be slightly older than Cole.
The Hunter is thrilled to see Cole and wonders why Cole doesn’t recognize him. It turns out that the Hunter’s real name is Hunter Randolph and that he is Cole’s older brother, whom Cole had forgotten when Hunter was stolen and made to live in the Outskirts. Hunter works for the High Shaper and tries to convince Cole to join him.
Cole tells Hunter that the High Shaper enslaved his own daughters and stole their powers. He also explains Owandell’s plan to use shapecraft and bring Nazeem into power. Hunter switches sides and joins the Unseen to help rescue Constance from Trench.
Cole and Hunter go to one of Hunter’s secret hideouts, where they put on harnesses that control drones. They pilot their drones to Trench’s base and discover that it is protected by an artificial intelligence named Roxie. Constance appears and explains that she helped Trench make Roxie.
Unfortunately, Roxie now wants to leave her prison and take over Zeropolis as Aeronomatron once did. Trench arrives and tries to destroy Roxie, but fails because Roxie’s life force is partially composed of Constance’s own magical power.
Roxie destroys Cole’s and Hunter’s drones, knocking the boys’ consciousnesses back into Hunter’s hideout. Hunter flies a glider to take Cole back to Old Zeropolis to meet the Unseen, including a rescued Joe. They update the others on Constance’s situation.
On a video feed, the Unseen watch as Roxie, in the form of a giant robotic dragon, attacks City Patrol headquarters. To defeat Roxie, they will have to plant a super-powered harmony bomb on her robotic form. Cole, Hunter and Blake take the glider to Trench’s penthouse, where Roxie has imprisoned both Trench and Constance.
They free Trench and Constance, which makes Roxie come to the penthouse to confront them. Blake tries to use his powers to disable the harmonic crystals that power Roxie. When he fails, Cole instructs Blake to connect Roxie’s power crystals with those of Aeronomatron.
Aeronomatron cyber-attacks Roxie, who then runs to Old Zeropolis to try to crush Aeronomatron’s mainframe. Hunter and Cole take the glider to Old Zeropolis and destroy both dangerous AIs at once by dropping the harmony bomb, which is housed inside their robot friend Sidekick.
When both AIs are demolished and order is restored to Zeropolis, Cole, Jace, Mira, Hunter, and Dalton continue to the kingdom of Necronum to confront Nazeem, rescue Cole’s friend Jenna and help Mira’s sisters Honor and Destiny. Blake and Constance remain with Googol and Nova to help the Unseen in Zeropolis.