This occurs if an entity (Lyoko Warrioravatar, monster, etc.) loses all of its life points. The entity vanishes from a virtual world. If a compatible program is available, the entity then materializes through the scanner again. However, if an entity falls into the Digital Sea, it is devirtualized forever.
Occasionally, a Lyoko Warrior nearly falls into the Digital Sea, only for another Warrior to save them by using friendly fire to devirtualize them before they fall into the Digital Sea. This has happened frequently enough that Jeremie commented that he needs to boost the devirtualization program in Saint Valentine's Day.
If a materializable entity is on a virtual world and a Return to the Past is launched, the entity will return to wherever it was on Earth at the time. If the entity cannot be materialized, due to it being a monster, a sector, Aelita (before Season 3), etc, then they will remain on the virtual world as if nothing happened.
There are several programs to move a warrior back from Lyoko to the real world. The operator (usually Jeremie or Aelita) is able to execute a series of commands to bring a given character back to the real world. Essentially, these programs are the reverse of the Virtualization program. Aelita's Materialization Program was one of these.
Different types of entities have different procedures for devirtualization.
Lyoko Warrioravatars: The avatar's pixels break apart and turn blue, then fade away, leaving only its vector lines. The vector lines then disappear.
Ninjas: The same as the Lyoko Warriors, but the pixels turn green.
Monsters (except for Guardians and the Kolossus): Seasons 1-4: The monster explodes into colored geometric objects, which flicker away. Some monsters blow into pieces and the remnants of their bodies disappear like in the case of Creepers or Tarantulas.
Monsters: Code Lyoko Evolution: They explode as red blocks, and then implode, with a similar effect to the circular laser. For a real life phenomenon that looks similar, observe a star undergoing a supernova, then collapsing into a black hole.
Scyphozoa: It fades away, as seen in The Lake. In Mutiny, it exploded as red blocks, and then imploded, just like other monsters in Evolution.
A Sector: The surface turns invisible and the vector lines disappear.
A Teleported Lyoko Warrior: Their body phases shortly before disappearing and reappearing in the Skid, unconscious.
In Spectromania, Jeremie explained that after someone is devirtualized, they cannot be virtualized again for twelve hours. However, in many cases during the original series, the Lyoko Warriors have been seen traveling to and from Lyoko in a span of less than 12 hours.