The Annex Program is a program that provided the protocol connection to Lyoko.
Apparently, only Franz Hopper and Aelita had the original version. The program allowed the user to possess cybernetic artificial intelligence, being able to read and understand computer files and binary codes allowing the user to access any interface, such as in towers, Sector Five, and the Cortex.
In Just in Time, Jeremie ran into an error in his materialization program and damaged Aelita's Annex Program. This would mean that if Aelita typed the Code: LYOKO in a tower, she would be reformatted and disappear for good. The program was damaged on a few other occasions; in Vertigo, when Jeremie injected Aelita with a faulty antivirus, and in Wreck Room, when Jeremie installed in an upgrade program for the William clone that caused the tower to stop recognizing the Annex Program, and Aelita in general, though she could still enter other towers. On both occasions, Aelita could not enter the tower until the problem was solved. The Annex Program was present in the Replikas and Aelita was able to use the Replikas' towers like in Lyoko. The Annex Program was copied by X.A.N.A. to William so he could enter the Code: X.A.N.A., as shown in Lab Rat.