The Keys of Lyoko played a role in the first and second seasons. X.A.N.A. wanted them in order to escape the Supercomputer. Franz Hopper split them in half and gave one half to Aelita. This gave her Creativity and most likely the Annex Program. Very little is known about them.
Description and Uses
The keys to Lyoko are programming codes that give bearers complete access to Lyoko's functions. They were given to Aelita by Franz Hopper before the events of Season 1, giving her the ability to deactivate Towers, and use her powers of Creativity. Besides that, the possessor of the Keys of Lyoko has complete access to the Supercomputer.
During Season 2, X.A.N.A. attempted multiple times to steal the Keys of Lyoko from Aelita 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. Also, by using the Scyphozoa, X.A.N.A. had the ability to fully steal Aelita's memories alongside the Keys of Lyoko.
For the remainder of the season two, the Lyoko Warriors tried to protect Aelita and the keys from X.A.N.A. However, in The Key, X.A.N.A manages to successfully steal the Keys of Lyoko, killing Aelita in the process. It has activated Towers in all four sectors, to finally 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 activated Towers in every sector. It was then that Franz Hopper stepped in to deactivate them to bring Lyoko back to life, and restore Aelita's full memory and humanity.
In the final season, X.A.N.A. had shown that the keys could be used to create new virtual worlds, dubbed Replikas, inside of other supercomputers that its own virus essence has infected. William also had the keys through his possessed link to X.A.N.A., allowing 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.