A few days after the first materialization of Aelita, Jeremy has created a new program: Vehicles For the Lyokowarriors : everyone has their own adapted to their own personality and that Aelita can borrow occasionally.

In addition, Jeremy has updated the scanning program, which finds the towers previously activated by X.A.N.A. The program, newly called the Superscan instantly detects every tower infected by the virus. This discovery has a lot of results: from now on, Aelita can stay with her friends on Earth and return when needed to Lyoko only for deactivating towers without staying with concern to monitor the pulsations.

Unfortunately for our heroes, X.A.N.A. also found some ways to surprise them: a new monster, the Tarantulas. Its strength is distinctly superior to the other common monsters: the Bloks, Kankrelats and Krabs. Because just one of these new creatures manages to beat the trio of warriors (cf Episode 27: New Order.)

The quartet of students don't remain satiated for long in welcoming their now almost-human friend. At the school, she is playing the role of Odd’s cousin: Aelita Stones. However, life as an Earthling is not so easy, and she often has disturbing visions of a past she never knew (Episode 27 "New Order"). These visions often appear near a particular place: The Hermitage, a deserted house with a secret corridor leading to the factory. This dilapidated building was once owned by an old Kadic teacher: Franz Hopper.

In the days that follow, the heroes discover the Sector 5, which they were unaware of existing. This Sector is very unlike the 4 others: it is accessed by the Lyoko warriors via the Transporter. The sector changes its appearance constantly. Within the sector is an interface where there is information about X.A.N.A. and monsters which defend only this sector... It seems to be XANA's home. (See the Places section.)

In addition to this area, a new monster appeared: the Scyphozoa. It seems to be unique and could never be destroyed. The defining feature of this monster is that has no weapons, but it can steal Aelita's memory. They are unaware at the time, but if the Scyphozoa were to succeed, XANA would escape from the supercomputer.

After the first meeting with the monster, things change drastically! While XANA still continues to launch many attacks, he always tries to steal Aelita's memory with this new monster. Only positive point, XANA and his monsters no longer take the risk of killing the pink-haired girl... The discovery of Carthage leaves open an opportunity for the heroes: to go on the offensive by visiting the central territory for discoveries about XANA.

A final new but equally important discovery: the teenagers manage to obtain the diary of Franz Hopper, following the trail of a key locker station out of a plush lying behind a poster in a room of the Hermitage (Episode 31 "Mister Puck"). It is a set of digital data stored in CDs but encrypted. Jeremy decides to decrypt them, half convinced that it could be used in the fight against XANA and especially in finding the antivirus. His hypothesis is confirmed by XANA’s attack to destroy the diary in the same episode that the heroes acquire it.

And the war continues, even more violently! The heroes discover a scary thing they had not considered: XANA grows in power with each return to the past that occurs. The supercomputer obtained even greater powers and becomes able, for example, to take control of a human being, it is Xanafication! Fortunately, the heroes' war skills increase with experience: they are able to face more monsters at the same time. Jeremy also makes some progress: he activates towers on his own (Episode 47 "Tip-Top Shape") and only uses returns to the past when there's absolute need and spends all his time either to decrypt Franz Hopper's diary or to work on the antivirus. The more he progresses, the more the name of Franz Hopper returns...

On the emotional level, Odd has relationships as short-lived as frequent. Jeremy and Aelita are still in love, but do not declare themselves as such. Aelita, more confident than before, steals a kiss from Jeremy (Episode 43 "XANA’s Kiss")!

For Yumi and Ulrich, the relationship becomes more convoluted. In addition to Sissi, a new player enters: William. This young man is in the same class as Yumi and has a crazy love for Yumi that cannot equal the jealousy it inspires in Ulrich. The young man is beautiful, romantic and very brave with a tendency towards provocation. The war between the young men is declared early on and confirmed in episode 36 "Marabounta." Troubles become more and more present, with provocations and brawls, and so forth (Episode 39 "A bad Turn"). Although in love with each other, Ulrich and Yumi insist not to declare it and do not make it very far without Sissi and William butting in...

The school year is almost over and XANA's attacks reach levels of violence without precedent. However, a new ally appears: Franz Hopper! The genius is in fact the creator of Lyoko, probably stuck in his own world, and he wants to get in touch with the heroes, which is not to the liking of XANA (Episode 50 "Contact"). Hopper steals control of one of XANA's activated towers at the decisive battle in Episode 51 "Revelations". With this help, the great Jeremy manages to decrypt the diary, which proves to be rather instructive!
The heroes learn many things about the creation of Lyoko. Hopper created it to counter a military program and also created XANA... but it escaped his control for an unknown reason. Cornered by mysterious men in black, the scientist decided to emigrate with his daughter to Lyoko, and this girl turns out to be Aelita!

Again, thanks to the newspaper, Jeremy learns two important things:
The first is Aelita doesn't have any virus, XANA had actually stolen a fragment from her: all of her memories which contained her childhood memories. It is kept on Carthage and can be recovered during an expedition. The visions of her past came from there.
The second is why XANA wants Aelita's memory: This memory contains the keys to Lyoko. With these, XANA could escape the supercomputer, thus eliminating any risk of being shut down with it.

The heroes then go in search of the missing fragment of Aelita's memories on Carthage. The expedition proved to be a failure! The warriors were devirtualizated and despite help from Hopper, Aelita falls into the tentacles of the Scyphozoa that finally manages to steal her memory. Aelita is left to the state of an empty shell, dead, while with a terrible roar, XANA frees himself from the supercomputer in the form of clouds and thick black smoke (Episode 52 "The Key").

Aelita is saved by Franz Hopper, her father, who brings her back to life at the same time as Lyoko by sacrificing himself. Using all his virtual energy, the fallen scientist gives her her missing fragment making her a full-fledged human.
Despite the efforts of our heroes, XANA escaped the supercomputer and threatens the world.
Our 5 friends are dismayed but their determination has never been greater! Together, they task themselves with the mission to continue fighting XANA.