The reasons for this change (as he had deleted viral Binomes by destroying ABC craft before) was not directly expressed on the show, but presumably it was the result of both Hexadecimal's reprogramming and his experiences of war-torn Mainframe.
As Command.Com, she had to fight two successive Viral Wars from a position of inferiority and was forced to make many morally grey decisions, such as having Enzo go into a Game and stay there until he grew into a new Matrix as an insurance policy.
It is a sign of her tactical skill that she was able to keep fighting against Megabyte, even with the loss of Enzo and the Principal Office, and then be able to cause some serious damage to Daemon.
The emotional stress of the Viral Wars took their toll after the defeat of Daemon, and she fell for Megabyte's plan to impersonate the original Bob out of a desire to get back to the good times and forget all the pain and horror.
Although he is quick to anger, he has still shown a desire to help those in need, and his quest to return to Mainframe has let him bring many systems back from the brink of annihilation.
Having spent so long apart from Mainframe, he is filled with the desire to defend his home by any means necessary, making it seem as though Matrix had become much more belligerent during the first part of Season 4, and this stance caused a great deal of friction between him and Bob in Daemon Rising.
The main antagonist of the series, Megabyte (voiced by Tony Jay) is a virus, originally operating out of the Silicon Tor in Sector 1000 and dominating most of G-Prime.
Megabyte plots constantly to corrupt and control Mainframe in order to turn it into his own domain, "Megaframe", and from there infect the Super-Computer and then take the entire Net.
Unfortunately, shortly afterwards a rampaging Hexadecimal took out the Firewall; resulting in war between the viruses that devastated G-Prime (including the Tor) and neighboring Sectors.
His plan worked so well, he almost ended up married to Dot, until Glitch retook Bob's stolen code and forced him back into his Viral form.
They once lifted and destroyed a very large bridge with ease in the episode Medusa, and both proved strong enough to punch the greatly sized Gigabyte out to the floor, or even high and far up in the sky.
Her powers include energy beams and fireballs, altering gravity (once causing Bob to stop and hover in midair) and being able to fly, shrugging off severe damage and controlling nulls (sprites downgraded to slug-like status for losing to the User in a game).
When removed (as in the episode "Painted Windows"), her power escapes and continues to do damage to her environment, and she will overload and be destroyed if the mask is not replaced.
In the episode End Prog, with the System about to restart, Bob insisted that Phong give Hex an Icon (or PID) to register her with the Principal Office so she would be backed up.
At the end of the episode "Sacrifice", with Bob in danger of dying, she had given away her new life as a pure Sprite to become her old reckless and insane viral self just to stop Daemon.
"Ill" again, Hex did not realize the severity of the situation until Bob told her that she would not survive the crash, and she made the decision to fragment herself into the Net as a "benign virus" to undo everything that Daemon had done.
Of all the characters depicted, only Fax Modem openly professed to deny the existence of the User, a position roundly regarded as wildly unorthodox and borderline insane.
Almost never seen, the only times he is explicitly shown on screen is when he is tied and completely covered up with rope in the episode "The Great Brain Robbery", and jumps in front of the camera in the third-season finale after the system is restored, having been apparently sped up he offers a fast and excited "Woo-hoo!"
An annoying, ambulatory television set from Bob's apartment who is constantly pitching bizarre products (like the famous Bucket-O-Nothing, free for only $99.99.99) or simply rambling on until somebody shouts at him to shut up.
Old Man Pearson (voiced by Long John Baldry) ran a waste disposal system (analogous to a Windows Recycle Bin) and data dump in Sector 1001.
A hacker extraordinaire with a sugary Southern accent, she is equipped with a katana to cut her enemies into small pieces, and a high-tech craft called Ship.
She first appears on-screen in "The Great Brain Robbery", hired as a mercenary by Megabyte (during the episode, she calls him "big guy" and "Megababe"); she turned against him when it became obvious she had been double-crossed and was endangering a young child.
Using his Gibson-Coil pike, he was able to teleport, knock over buildings, wield energy bludgeons, and imprison Bob's Keytool, Glitch, behind a force field.
She also appeared highly naive, such as believing Enzo's lies about being a Guardian (though she later admitted she always knew the truth, but didn't care because of her feelings for him).
Luckily for Mainframe, Hexadecimal's power had been drained at the time and Gigabyte was not at full strength, forced to feed off the energy of individual Sprites.
After being partially cured by Bob's incomplete Guardian code, Turbo provided valuable information which helped Mainframe fight back against the super-virus.
She speaks in a French accent and calls Mike the TV "Michel", and is depicted in the style of Joan of Arc, a petite female holy warrior.
The resulting explosion nullified Welman, split Gigabyte into the entities Hexadecimal and Megabyte, and destroyed Mainframe's sister city, the ruins of which were later to be known as Lost Angles.
Since Welman's ability to assert his personality is directly connected to Hexadecimal's well-being, she imbued young Enzo's icon with the same function before sacrificing herself to undo Daemon's Net-wide infection.
When Enzo came in contact with him, Welman regained his sentient mind once more, and became able to move around by controlling a "Null-Bot", which he used to walk his daughter Dot down the aisle at her wedding.