In Paris, Tai, a powerful program called a Keeper, narrates the death of the main protagonist's father. He and a group of Keepers walk in a city in Cyberspace, but are ambushed by Tetsuo Shima, the evil leader of the tyrannical Dexicans. EJ's father attempts to defeat the Sentinels with his hatchets, but Tetsuo kills him. This is seen by Tai himself and his younger but telekinetic sister, Kari.

Fourteen years later, his son, Esteban Jose Taboada (EJ for short), develops into a kind and intelligent yet short-tempered young man who has been fighting the Dexicans his entire life. A trio of friends—Timothy, Algernard, and Secilia—pay EJ a visit, and suddenly inform him that the Dexicans are attacking. This frustrates EJ, who says "For years I've worked to purge the world of those wretched Dexicans, and now the streets teem with even more power hungry jerks that threaten law and order." Kaneda, the leader of the Hexicans, reveals that the Dexicans are attacking on a global scale to atone for Shockwave's death. In Tokyo, EJ is attacked by the crowd after Kaneda, the leader of the Hexicans, starts a riot. Kaneda is captured and cannot help, but Kari intervenes by freeing EJ and Kaneda, and uses her psychic powers to evade arrest.

In the outskirts of Mexico, Secilia follows EJ, who is eager to meet her family members, only to be followed herself by Grill. He refuses to arrest her for alleged witchcraft inside and instead has her confined to a cathedral. EJ finds Adrian, Secilia's brother, who helps her escape Notre Dame out of gratitude for defending him. 

In Fiji, Timothy entrusts EJ to hold a pendant containing a map to the Keepers' hideout, the Court of Miracles. EJ then fights a trio of Dexicans and goes back to Cyber Lake Wales.

In Canada, Tetsuo develops lustful feelings for Maribel and, upon realizing them, begs someone to save him from her "spell" to avoid eternal damnation. When Tetsuo discovers that she escaped, he instigates a city-wide manhunt for her which involves setting fire to countless houses in his way. A Dexican named King Dedede discovers Tetsuo's evil reputation and defies him, who then sentences him to death. Dedede is struck by an arrow and falls into a river, but Kirby rescues him and takes him to Tuvalu for refuge.

Tetsuo returns to the Virus later that night and discovers that Adrian helped EJ escape. He bluffs to Kaneda saying that he knows about the Court of Miracles and that he intends to attack at dawn. Using the map Timothy gave him, the Hexicans and Hexkids find the court in Port Mystic in Japan to warn the Keepers, only for Tetsuo to follow them and capture everyone present. 

At Notre Dame, Tetsuo prepares to burn Maribel and Secilia at the stake after Maribel rejects his advances, but EJ rescues them and brings her to the cathedral. EJ is given orders by Maribel to deal with the Dexicans while she heals Secilia. Kaneda releases the Hexkids and rallies the Hexicans against Tetsuo and his minions, who try to break into the cathedral. EJ, Timothy, AJ, Emma and Ben pour molten copper onto the streets to ensure no one enters, but Tetsuo successfully manages to enter. Tetsuo pursues EJ and Secilia to the balcony where he and EJ both fall over the edge, while Timothy, Maribel, Secilia, AJ, Ben and Emma try to save EJ. Tetsuo climbs a gargoyle to try to kill off Timothy, AJ, Ben, Maribel, Secilia and Emma, but Kari accidentally casts an animation spell on a statue of EJ's father. It suddenly comes to life, chokes Tetsuo and drops off Notre Dame's balcony. Because of this, Tetsuo falls to his death in the molten copper, while EJ is caught in time by Kaneda on a lower floor. Afterward, EJ comes to accept that AJ and another girl are in love, and he gives them his blessing. EJ, the Hexicans, and his friends return to Cyber Lake Wales and hail them as heroes. 

In a post-credits scene, EJ tells the Hexkids that he will be going to Africa to search for the spirit of Captain Falcon, who died the last film, and leaves Timothy and Secilia in charge before leaving. However, after he leaves, Secilia senses a psychic disturbance that will presumably end the world in a week, preparing the characters for the events of Cybergate: Dark of the Moon.