This is the third part of a four-part movie:
While they are talking, Kilobyte breaks free. Dixie uses her keytool, Glitch, to report "a 403 (viral upgrade) in progress". She warns Central that the upgrade is skipping a generation; the Virus now has the ability to fly, transfinite power reserves, and the ability to survive a narrow-beam laser through the skull. The Virus knocks cadet Bob out and kills the female Guardian.
It starts toward Bob to finish him off, when a circle of energy appears. Skinny Kilobyte transforms into the wide-chested Gigabyte, then he and the circular gateway disappear.
Present time: In the brig, Turbo tells Mouse that Ray the Surfer has heard The Word and is waiting for her to drop the Firewall. To Bob, Turbo says that all his radical theories are correct; there are benign Viruses that can do good. The question of Turbo's keytool, Copeland, comes up. It turns out that all other Guardians are incomplete as their keytools abandoned the Guardians at time of infection. Glitch Bob is the only Guardian + keytool pair left. He's the only one who can create portals.
Glitch Bob fires a burst of code at Turbo and is able to drive off most of Daemon's influence. Turbo is not completely cured, but is able to provide information to Bob and Dot. Daemon's function is to provide "unity" to the entire Net.
Phong explains how Hex changed from a Virus to a Sprite. The power drain required to make all the Guardian ships go away left her open to a virus-scan by the User. She tried to use the Nulls to shield her, but they ran away when the Game Cube arrived, allowing the User's virus disinfectant to succeed. Hex lost her powers, but is still able to communicate with Nulls.
A WWF Game cube shows how Matrix has turned into a beast without AndrAIa. AndrAIa, on the other hand, is merely melancholy in the Supercomputer. Daemon is surprised to hear AndrAIa's statement that love conquers all. (The Super-Virus was not programmed for love.) Daecon and the others love her, but that's not the same.
Daecon: "I have failed you, my Lady."
Daemon: "CALL 101."
Daecon: "101. 100. 11. 10. 01. 0." (5, 4, 3, 2, 1, 0)
Daecon dematerializes, Daemon soaks up his spirit.
Dot drives Hex to Lost Angles in Bob's car. When asked, Dot adamantly states that she and Bob are "just friends". On the ground, the idea is to gather the Nulls together to bring back Dot's father. But without Nibbles, it doesn't work and Hex wants to give it up. When Dot asks if she would give up if it were her father, Hex makes the startling statement that she was born in the explosion that created Lost Angles.
Flashback: Professor Matrix, after demonstrating that a system has been detected via PING, executes the Gateway command. It brings in the nasty Virus, who declares, "I am become Gigabyte, destroyer of systems!" The revolving Gateway cleaves him in twain, begetting Megabyte and Hexadecimal. It also triggers the explosion that wipes out the Auditorium, transforms the Twin City into Lost Angles, and converts the Sprites into Nulls.
Present: Hex says "In a strange way, your father saved my life. Or rather, gave me life. I'll try again, 'sister'." She gathers the Nulls together in a full-sized man shape. It starts talking once Nibbles has joined to make its head. Welman Matrix is able to talk to his daughter, but she cannot touch him (due to the energy-sucking nature of the Nulls).
Phong has bad news regarding Glitch Bob's medical examination. Bob already knows: the merge with his keytool was not completely successfull due to the damage suffered by Glitch before the merge. But this little chat is interrupted by a more pressing problem. The system is on-line - Mouse and Matrix are foolhardily going after their lovers. Mouse knows the Firewall codes but they won't remain a secret once she's infected.
Dot commands her father to rebuild the Gateway with Phong's help. Bob is told to research why it code blast didn't work, and Turbo to spill the beans on Daemon. "We're running out of time, and you can never trust a Virus."
In the Supercomputer, Matrix strides boldly into the throne room, commands Gun to target the woman sitting there, but the person there is AndrAIa. Daemon appears and Matrix fires a bullet with her name on it. It is shown in slow motion, leaving visible shock waves behind it, but stops just in front of her face and harms her not. From the curtains, Mouse rushes in to behead the Virus, but her katana sword shatters. Daemon touches the floor and instantly infects them both.
Turbo tries to convince Bob that Daemon must be destroyed. Bob points out that Hexadecimal was cured, he still believes that he could have turned Megabyte in time. "After what his genesis did to Mainframe's Twin City, after what he did to your partner?"
Flashback: Cadet Bob holding the dying Guarding Dixon in his arms. Glitch indicates her energy is gone, and disconnects as she dematerializes. The key tool floats up, decides that Bob is worthy to carry on, and attaches to Bob's arm, exchanging codes.
Tears have broken out all over the damaged Mainframe. Bob arrives via a portal and immediately starts mending them. A hysterical Dot misunderstands his appology, initially blames the destruction on the Cadet/Guardian. Turbo (wearing the red suit of the Prime Guardian) and two other veteran Guardians also lend a hand.
Present: Bob and Turbo in the brig.
Turbo: "The Net has grown exponentially. It's becoming impossible to police. In a strange way, Daemon was right."
Turbo: "She's trying to bring order to chaos. Now, isn't that our prime function?"
Bob: "She wants unity. One voice, one way. The Net is supposed to be varied, diverse."
Turbo: "Maybe it's too diverse."
The episode ends with Turbo asking why Bob's code didn't cure him.