The gang has planned a routine data gathering mission in the Cortex. However, Ulrich opts out of the mission when he finds out that Yumi wrote some negative things about him. While in the Cortex being attacked by Ninjas, Yumi can't stop thinking about Ulrich. She gets herself devirtualized on purpose just to go talk to him and work things out. The two soon reconcile. Meanwhile, a Ninja, not defeated in the fight in the Cortex, follows the Megapod back to the Skid, then hangs onto the Skid all the way back to the hangar in Sector Five. William ends up being left alone to fend off the Ninja, which is heading for the Core of Lyoko itself. Ulrich is called in and easily destroys the Ninja with his sabers, but it plants a sinister-looking device on the bottom of a platform in Sector Five before it disappears.

Nouvelle mission d'enquête sur le Cortex pour localiser le supercalculateur qui génère le territoire, où William, Yumi, Odd et Aelita affontent les Ninjas. Pendant ce temps, Ulrich reste au lycée car il s'est brouillé avec Yumi à cause d'un texte où elle le décrit. Au retour du groupe sur Lyoko, ils découvrent qu'un Ninja les a suivis sur Lyoko.

Para localizar el superordenador de Ikonov y destruirlo, Jeremy ha desarrollado un programa que los Guerreros de Lyoko van a introducir en el núcleo de Cortex. El plan sale bien cuando van a Lyoko, son seguidos por un ninja de Ikonov Ninja. Y sólo en el Quinto Sector son conscientes de su presencia. Una terrible lucha comienza entonces para impedir el acceso al Ninja al núcleo de Lyoko y todos los datos que contiene.