The game’s scenario runs parallel to that of season 4 of Code Lyoko without following it exactly. The heroes, with their new equipment, must rescue William who has fallen into XANA’s clutches.
Unlike the series, the game offers many new ideas such as the appearance of new monsters and a new territory.
The game’s story begins with the completion of Jeremy’s recreation of Lyoko and the creation of the Skidbladnir, the virtual ship/submarine that will allow Lyoko Warriors to dive into the Digital Sea in search of William and of XANA.
It is during the ship’s inauguration trip that the heroes will discover the Replikas, virtual worlds created by XANA; each of them is a replica of one of Lyoko’s surface territories. While thwarting XANA’s attacks on Earth, the Lyoko Warriors will attack the Replikas.