This article is not canon
Paradigms Lost is part of a 3 part webcomic series posted on the Reboot.com website. It is about the events after Megabyte takes over the Principal Office and announces his plans for revenge on the leaders of Mainframe. (ReBoot: My Two Bobs)
Bob and Matrix rescue Phong, just as zombinomes nearly corner them. When they arrive in a safe zone, Phong is surprised to learn that they are evacuating Mainframe to the Super Computer. Bob explains that during his disappearance, viral outbreaks began appearing all over the Net, meaning the Guardian Collective is spread out. Worse, the Users haven't been heard from, no Games, or upgrades.
In the Super Computer, Bob talks to Turbo, who is disturbed that he didn't delete the zombinomes. Bob insists that they are citizens and that he could cure them only for Turbo to cut him off, pointing out that he had never once been able to reprogram a virus into a benign Sprite. Because of this, many Guardians are calling out for "Viral Rights" leaving viruses to attack unchecked. Turbo leaves, calling Bob a viral sympathizer.
At the initiation ceremony, Turbo presents their star pupil, Enzo, his Key Tool, Sparc, who will only work for him when he proves he has "the heart of a Guardian". Enzo then gives a rousing speech, citing the Guardian motto, "To Mend and Defend". As the crowd cheers, Bob leaves. While the celebration party begins, Turbo talks with Matrix, asking if he'd consider joining the Guardians as well, but he refuses. Turbo still gives him some device that he may use one day.
Arriving in Mainframe, Bob creates a battle armor, determined to finish his battle with Megabyte once and for all. On his way to the Principal Office, he is interrupted by a vidWindow from Turbo, telling him to come to another system, where he is meeting the Code Masters. Though surprised at learning of the cult's reappearance, Bob joins Turbo just as the Codemasters arrive. Their leader, the Guildmaster, reveals they have created a program called Gnosis that can permanently erase all virus in the Net. The conversation is recorded by a fly who sends the footage back to Megabyte. Megabyte orders Herr Doktor to construct a shield against Gnosis, threatening him with deletion and substitution by Welman Matrix.
Super Computer scientists analyze Gnosis, finding that it is powerful and incorruptible. Bob says they must first test it on Mainframe. It seemingly kills Megabyte and cures all of the zombinomes. Once all of Mainframe is healed, Gnosis is used on the Net, wiping out all viruses instantly. After doing a complete scan, Turbo says the Guardians can take a well deserved vacation. Matrix drops the device in the garbage; Bob and Dot are going to do what they should've done a long time ago - get married.
As soon as Turbo leaves, the Guildmaster orders Gnosis to begin "Phase Two".
Part 2: The Day the Net Stood Still
Mike the TV (in an Elvis costume) quickly marries Bob and Dot finally. Their happiness is short-lived when Lens crashes in. He tells the Guardian that Gnosis has evolved before passing out.
In the Super Computer, Gnosis is still gathering data on the Net. It determines that the Guardians are a threat to scanning and that the only option is to exterminate them.
In a Mainframe hospital, the others learn from Lens that the Guildmaster had integrated Gnosis to the Super Computer. Lens objected, resulting in the acolytes attacking him, but he managed to escape. He explains that the Codemasters gain power from the Code Command Words, of which few are known. The Guildmaster intends to unlock all codes to form the Codex, and achieve ultimate power. When the Guildmaster was only an apprentice, the Codemasters' current leaders looked down on his views. But now, he is in charge.
Bob and his friends prepare to storm the Super Computer, joined by Lens. When they reach the Super Computer with Turbo, they find that Gnosis has formed a face out of Sprites, determining all threats to completion. When the Guildmaster reaffirms his supremacy over it, Gnosis simply deletes his master. It then disables all of the Key Tools and reformats the Codemasters into Avatars. They are able to delete Ray, Mouse and Turbo, while the rest are able to escape. The Avatars then attack Enzo's class, shooting him and his entire class and then proceed to Mainframe. Matrix and AndrAIa locate the mysterious device Matrix got from Turbo that he had thrown away. He accidentally activates it, revealing a message from Turbo. Should the Guardians and Keytools ever fail, a new order must take its place.
Deep beneath the Super Computer, Lens reveals to Bob the Codemaster City, which they've managed to build under the Guardians' notice. Because Gnosis disable Glitch, Bob will need another way to fight. He first thinks he will be trained to become a Codemaster, but Lens affirms that it would take years and gives him a few Code words. At night, while they sleep, Bob hears a voice asking for help originating from a jungle of cables. What he finds is something unlike anything in the Net.
Elsewhere in the cables, Enzo and a number of Sprites are hung upside down and gagged by the cables. Enzo is able to free himself with his icon and heads into Gnosis' throne room where he is grabbed by a very much alive Megabyte.
Part 3: Apocalypse Gnosis
Mainframe is enslaved by the Avatars, with cables all over it forcing the hapless citizens to push turbines sending power through a portal. Dot is cornered by Avatars, who reveal their number faces are similar to Gnosis'. They demand that more power and workforce be sent to Gnosis but Dot protest that they'll fragment. The Avatars determine that she is to be reformatted before she is saved by a trenchcoat Sprite, whose guns fire through the Avatars' faces. Matrix and AndrAIa are revealed to be with the stranger, informing Dot that his name is Vector, a member of a team put together by Turbo.
Back at the cables near the Codemaster city, Bob meets Exidy, a twelve armed winged Sprite who was sent to restore order but wound up trapped by conduits that destabilized her program. She explains that the use of the Code is forbidden, as she is the Source, and that the Codemasters have used it to push things to the brink of destruction. Only Guardians can use it safely to maintain balance otherwise the Users would abandon them; the Users are currently vacationing in the Web. Exidy then stops talking and informs Bob she will grant him the power of the Code to destroy Gnosis and afterwards set her free. However, she warns him that the power comes with a price.
Elsewhere, Megabyte is bowing before Gnosis and it asks why Enzo is in its presence. Enzo asks back as to why it is deleting people; Megabyte answers that it is gathering processing speed for the Codex completion, which will grant them the power of the Users. Accidentally, Enzo gives them the idea to conquer the Net, even the Web.
Back in the processing plant, Matrix and AndrAIa rescue Hack and Slash but are surrounded by Avatars. Suddenly, they are destroyed by Bob, who has learned how to use the Code from Lens, who is quite surprised by how quickly he has mastered it. Suddenly, they are attacked by Enzo. Bob uses a Code (//>CACHE.EXE) to put up a barrier but Lens shoots Enzo, deleting him. Matrix is outraged at Lens who goes to explain that it was not the real Enzo. He theorizes that Gnosis is an amalgamation of Sprites that were supposedly deleted. Considering that the Avatar's weapons are similar to the Codemasters' Gibson Coil Pikes, the Guildmaster probably set things up so that the victims were sent directly to Gnosis. This means that Enzo and everyone else is still alive. After taking up Pearson's data dump at a rebel hideout, Bob prepares to be decompiled. As he and Dot come close for a good-bye kiss, Lens zaps him, not wanting to see it.
Back at the Supercomputer, Gnosis has already conquered 37 systems. Enzo tries pleading with Gnosis for it to find a more peaceful solution to achieve more power, like cooperating. Tired of the boy's meddling, Megabyte grabs Enzo. At this moment, the Keytool Sparc dubs Enzo worthy and grants him big muscles. Suddenly, Megabyte is deleted by Bob and as he is about to do the same to Gnosis, Enzo asks for a chance to talk to it first. He requests that Gnosis undo everything it had done, including all the decompiled Sprites.
Mouse, Ray Tracer and Turbo are all restored, along with many other sprites Gnosis decompiled.
Bob then returns to free Exidy, only for Lens to intervene, stating that the Code can be used to bring peace to the Net and the Web; Bob is worried that it might create another Gnosis. Exidy asks Lens if she is a mistake and he responds by freeing her.