Traveling into the digital sea inside their submersible submarine (which they had called the Skidbladnir), the five Lyoko Warriors come across another virtual world near Lyoko called the Cortex. However, as this new virtual region is ever-changing and chaotic, Jeremie programs a secondary viechile called the Megapod with Odd as its pilot. In the very center, lies the Core/Heart of the Cortex itself and by investigating further, they all discover a new enemy just as dangerous as X.A.N.A. Professor Tyron − who seems unaware of X.A.N.A.'s existence within his own supercomputer. The Lyoko warriors must deal with constructing a strong enough virus to completely exterminate X.A.N.A. and stop Tyron, as well as the powerful team of Ninjas his virtualizes onto the Cortex to battle the five Lyoko avatars.