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The Keys to Lyoko play a major role in the Season 2, as X.A.N.A. wanted them in order to escape the supercomputer.

Description[]

According to Sophie Decroisette, the Keys to Lyoko are the source codes and plans of the supercomputer itself.[1] The keys provide bearers complete access to Lyoko's functions, such as access to the interface in Sector Five and towers activated by X.A.N.A.. They were given to Aelita by Franz Hopper, who also held them, giving her the ability to deactivate Towers and use her powers of Creativity.

During Season 2, X.A.N.A. frequently attempted to steal the Keys to Lyoko from Aelita through the Scyphozoa in order to escape from the supercomputer and gain access to the world network. To do this, X.A.N.A. stole a fragment of Aelita's memories, linking her to the supercomputer to prevent X.A.N.A's deactivation.

Throughout the second season, the Lyoko Warriors tried to protect Aelita and the keys from X.A.N.A., though they were unware of the keys' existence until after decoding Franz Hopper's diary in Revelation. However, in The Key, X.A.N.A. finally managed to steal Aelita's Keys to Lyoko, killing her in the process. It activated towers in all four sectors to escape and gain access to the world network. X.A.N.A. could also perpetually render the virtual world inactive to the four sectors with the keys using the same towers in every sector. It was then that Franz Hopper stepped in to deactivate them and bring Lyoko back to life, as well as restore Aelita's memories and humanity.

In Season 4, it is revealed that X.A.N.A. had also used the keys to create copies of Lyoko, dubbed Replikas, inside other supercomputers it infected. William also seemed to have access to the keys through his possessed link to X.A.N.A. This allowed him to use the Annex Program to control towers like Aelita, which provides X.A.N.A. with the means to bypass the security of towers that it cannot access on its own, by using William's virtual avatar.

As of Evolution, Yumi and at one point Odd and Ulrich held the Keys to Lyoko, that were given to them by X.A.N.A. via his source codes.

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