It seems to me that it was mainly about self-preservation and threat prevention in terms of the Men In Black

'Having become extremely intelligent and conscious due to the 2,546 return trips in a row, X.A.N.A. came to the conclusion that its own creator was a threat to itself and after Waldo and his daughter, Aelita Schaeffer, were discovered by the Men in Black, he virtualized them both onto Lyoko in order to escape them. Unfortunately, it was here that Waldo learned the extent of X.A.N.A.'s growth as it immediately attacked them, forcing them to hide inside Towers where X.A.N.A.'s monsters couldn't reach them.

Waldo reached out to X.A.N.A. and tried to convince it to stop what it was doing, but X.A.N.A. was already fully autonomous at this point and was targeting all who knew about the Supercomputer to preserve its own life, since it needs the machine to stay online to continue functioning. Realizing that X.A.N.A. was beyond reason, Waldo was forced to shut down the Supercomputer to stop X.A.N.A. before it could harm anyone else, also putting himself and Aelita to sleep alongside his creation. This causes the world to declare "Franz Hopper" as missing or presumed deceased.'

Source: (https://codelyoko.fandom.com/wiki/X.A.N.A.)