A new girl-genius and highly gifted teenage girl named Laura Gauthier tries to join the quintet at Kadic Academy. She humiliates Jeremy by correcting his mistakes on a complex exercise in class. Aelita suddenly is resentful and suspicious of this new girl, who seems to want to discover their secret. Meanwhile, Jeremy informs his four friends that he has programmed a new vehicle that is made for travelling through the Cortex easily called the Megapod. Once on the Cortex, they are impressed by the new cruiser, which Yumi ends up driving. Unfortunately, Laura follows William to the factory and discovers the lab and Supercomputer, which she is very interested in. During a battle with several Krabes, Aelita, Odd and Ulrich are devirtualized, leaving Yumi trapped in the Megapod. With Laura's help, Jeremy fixes the bugged vehicle and Yumi is returned to Earth just before the Megapod falls into the Digital Sea.

William is yet again rejected by the group, but when he asks Yumi for her help on a project she happily agrees, much to Ulrich's disdain. The dislike between the two grows when XANA creates a spectre of William to attack Yumi, and the two almost have a fistfight in the gym. Soon after deactivating the tower, another one appears. Odd, Aelita and Yumi cannot return to Lyoko as they were there not long ago, so it's up to Ulrich and William to put their differences aside and get Ulrich to the tower to deactivate it. At first the two are showing off and trying to outdo each other, but after William saves Ulrich from falling into the Digital Sea, they call a truce, allowing Ulrich to deactivate the tower. Once back on Earth, William is fully accepted into the group as the sixth Lyoko warrior.

Jeremy and Aelita program false source codes that will destroy any specter that tries to take them from a Lyoko Warrior, and tests it using Ulrich as a guinea pig. Ulrich is told to wait at school until he spots a specter and deliberately touch it to transfer the fake source codes to it to test if they work. A specter with hypnotic abilities appears the same day. If the specter manages to catch someone's gaze, it can send them into a trance-like state which the specter can use to approach a Lyoko Warrior and take their actual source codes without them fighting back. Ulrich manages to test the false source codes and destroys the specter, but it knocks him unconscious for a while. Jeremy decides not to try it again as it is too risky.

The gang return to the Cortex to get data on the mysterious Ninjas. Ulrich opts out of the mission because he has a karate competition to attend, and Jim won't let him skip it. The others don't fare well against the Ninjas until Ulrich arrives, offering them advice that Jim passed on to him; be unexpected. With the advice given by Ulrich, and a new-and-improved, unusually effective bo staff weapon programmed for Yumi, she manages to defeat the three Ninjas easily and gathers the data. In it they find a video clip of Professor Tyron addressing several humans dressed in ninja-like costumes. Ulrich wins the competition and gives his trophy to Jim, thanking him greatly for his advice.

A computer error causes the science test scores at Kadic to be messed up, as well as bugging up the rest of the computer system with it. Jeremy is alerted to an activated tower and he, Aelita, Odd, Ulrich and Laura go to the lab to check it out. Laura's dad is called to the school as a result of the marks mix-up and he calls her back to the principal's office. He expresses his doubt in her abilities and his wish for her to go to another school. Laura insists on staying, deciding to show him the Supercomputer as proof of what she can do. Meanwhile, the others explore Lyoko looking for the activated tower that's nowhere to be found. Jeremy eventually picks it up in the Cortex and sends them there to take care of it. When Laura and her dad arrive, Aelita goes back to the lab to get them out of Jeremy's way so the mission can be completed. The tower is deactivated and a return to the past is launched.

Jeremy manages to develop a program that will allow the gang to hack Tyron's surveillance system and spy on him, both using video and sound, and potentially speak to Anthea. When the gang go to the Cortex to implement it, all but Aelita are devirtualized by Ninjas when they tip off an unforeseen security system. Aelita opts to stay in the Cortex's core to wait for her mother to appear, asking for a clone to replace her at the school while she's gone, which causes enough problems of its own. In the end, Aelita is able to speak to her mother, convincing her that she is alive before she, too, is devirtualized by Ninjas. The experience initially leaves her feeling very sad, but after Jeremy assures her that Anthea got the message, her spirits are rekindled.

We don't have an overview translated in English. Help us expand our database by adding one.