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Deletion (sometimes also known as Eternal Virtualization) occurs when an entity comes into contact with the Digital Sea. The DNA and coding of the person that dropped into the Digital Sea is then dropped by the qubits of the Supercomputer, spreading the DNA and coding for the person virtual shell and physical body across the network into many millions of parts, effectively killing them. It is one of the things most feared by the Lyoko Warriors. Many close calls have been had, with Yumi being the first one who has ever fell into it in Cruel Dilemma. She was saved by Jeremie's one shot devirtualization program, which relocated, recompiled, and reconstructed Yumi's physical and mental body, at the cost of not being able to devirtualize Aelita yet.

When something falls into the Digital Sea, a beautiful, glowing white column of light emanates from the part of the Digital Sea which the object fell into.

Falling into the Digital Sea would result in the deletion of the subject. The only exceptions to this effect are the Skidbladnir, X.A.N.A. William and Franz Hopper, and any type of monster designed specifically to live in the Digital Sea, such as Kongres, Sharks and Kalamar. Falling into the celestial dome in the exterior of Sector Five would have the same effects as falling into the Digital Sea.

Being devirtualized without the scanners being online would also cause deletion, as the security protocol that regulates forced devirtualization will not be overridden by any command. It will attempt to discharge the quantum memory in use holding the matter and brain activity of the person, and upon realizing a scanner is not connected, it will auto-dump the quibits being used to hold the massive amount of data that the human makeup is. This ensures permanent virtualization.

The only thing so far to have brought back a deleted character is Jeremie's one-shot materialization program, but there is no way that he can rewrite the program, from not knowing the code that was typed in by Odd accidentally dropping candy on the keyboard.

In Distant Memory, Aelita was thrown into the Digital Sea, and the white column of light was seen, meaning that she was deleted. However, Franz Hopper brought her back onto safe land, which may possibly mean that Franz Hopper is able to reconstruct physical bodies after they have fallen into the Digital Sea.

Deletion can also occur to nonliving objects, such as data or surfaces of sectors or even the virtual worlds themselves, by the means of anyone at the Factory Interface or X.A.N.A. voluntarily deleting the object in question. Deletion can also be involuntary, such as the destruction of a replika, in which the destruction of the supercomputer hosting it means that the replika cannot exist because there is nothing to contain the data.

X.A.N.A. used his own code to delete sectors of Lyoko in Season 3. In some episodes, when the supercomputer is damaged or inactive, parts of or the entire sector of Lyoko would disappear, such as in Common Interest where Ulrich and Odd nearly fell into the Digital Sea because the nuclear battery powering the supercomputer was dying and the Ice Sector was erasing itself, and in False Lead where the X.A.N.A. possessed man in black was trying to fry the circuits of supercomputer, which caused parts of the Ice Sector or the pathways in the Mountain Sector to disappear randomly, same with the vehicles.

Things that are projected using towers, such as specters, will disappear if the tower generating them is deactivated. However, if the specter manages to be virtualized on Lyoko before the tower generating it is deactivated, it will be sustained and not disappear.