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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
ReBoot
Phong knew all along that Enzo, AndrAIa and Friskit survived.
In "Number 7", Matrix's dream/nightmare was created by Phong through some psychic connection, similar to with Dot in "Identity Crisis, Part 2". The dream Phong is the REAL Phong.

This may have happened inadvertently while Phong is being tortured by Megabyte.
  • Or, maybe it was the result of what Phong did to Dot? The device was supposed to send waves into the past and future. The past effects we saw, Dot hallucinating, but maybe this was the future waves? Maybe this is when the flash forward Dot was having would have actually taken place?

Mainframe's User is a little kid.
Plays games all the time, never erased the RAM which spawns the game characters in System Crash, only updated the system files once, never ran a virus scan before the system crashed, didn't even try to fix the system when Megabyte destroyed it, and after the system crashed he only types YES when the computer asked for a system restore. The user was simply to young to know how to do anything on a computer other than play games.
  • You do realize that the user only experienced 2-3 days over the course of the show's entire run, right? And updates tend to be done automatically when the system is online.
    • In that case, the User has been playing a metric ass-ton of games in that little a time. Maybe the game cubes represent flash games?
      • Neither the updates nor flash games were popular when the series was made.
  • That explains why he couldn't move that tank in the beginning of "Identity Crisis, part 1". And the fact that it's an old game like Enzo said.
  • Also, his parents probably upgrade for him. But the Mainframers don't know that, which is why they think he only upgrades occasionally.

Games are only harmful to systems that already have a viral infection
That is, games only compound the system errors caused by Viruses, the most common and prominent of which is Nullification. Systems that are clean don't have anything to fear from losing games but viruses are so prevalent and the effects of their infestation are so ingrained into public consciousness that no system dares running the risk of losing a game.

Mainframe does not have one User
But several, it's a family computer that everyone is taking turns using and playing with. This is why the User seems so inconsistent, there is actually one one tech-savvy person in the family and everyone else is screwing around, playing games, downloading viruses from the net and generally causing problems for everyone else.
  • It's also possible that Mainframe is a public computer in a school or library that the patrons are using improperly.
  • The name is very likely literal; the system may just be a mainframe computer. Such devices tend to use timesharing operating systems and all use of the system would be through terminal machines. Such systems are designed to remain operational constantly, and only require occasional maintenance from an administrator.

ABC was afraid that CGI would take over Western Animation.
All the Executive Meddling ABC did to ReBoot was an attempt to force the show to fail and kill the medium before Follow the Leader took effect and spawned a wave of CGI shows that would replace traditional Western Animation. While ReBoot survived the meddling, ABC succeeded in preventing Follow the Leader and delayed the wave of CGI shows for about a decade. ABC's motive for this was to maintain the Animation Age Ghetto by preserving the Status Quo of Western Animation.
  • Mainframe also ended up making Beast Wars only a few years later in syndication, which helped popularize the idea of an all CGI animated series and led to the boom in CGI animation that persists to this day. With Beast Wars they still had Executive Meddling to deal with, but it seems almost kind and good-natured compared to some of the hoops Reboot had to go through, and most of that was because there was franchise history and continuity to deal with rather than outright censorship.

The User is a genuine Eldritch Abomination.
And I don't mean on a Humans Are Cthulhu scale. Nothing the User does and nothing about the Net and the Web make any sense when applied to our computers. It's easier to believe that sprites and binomes are human-scale entities in a universe run by creatures that would drive real-world humans mad on sight.
  • Alternatively, The User IS Cthulhu, and Mainframe exists in an Eldritch Computer that follows a completely different set of rules that don't make sense to us, but make perfect sense for Cthulhu.

Hexadecimal isn't a true virus
She's a living viral upgrade. When Kilobyte upgraded to Gigabyte it was stated to have skipped a generation. However, as it was upgrading it was teleported away by Welman Matrix and seperated into two viruses. Megabyte is the real virus, the skipped generation, strong, persistent and infectious. Hexadecimal is the interrupted upgrade, she's raw power given form, her chaotic behaviour is due to a lack of purpose. Notice how, throughout the entire series, Hexadecimal lacks a function, no other character has this problem. Every single virus we see is on a mission to infect or destroy but Hexadecimal just sits around until she gets bored and then stirs up some trouble, not even seeming particularly bothered when she is ultimately thwarted and even switches sides without much thought or effort. Further notice that Gigabyte really is little more than Megabyte with Hexadecimal's powers.
  • Unless spreading chaos IS her function. It would explain why Gigabyte doesn't have the exact same function as Megabyte. Function: infect and conquer + spread chaos = destroy systems.

Mainframe's User rents all of his/her games.
Assuming all of those games run off a disk and are not installed into the computer this explains why the User rarely plays the same game twice. He/She rents a game, plays once and loses, says WTF this game sucks, and returns the game immediately.

Number 7 Wasn't a dream.
That system was really a Playstation and The User had loaded the ReBoot video game for the console. But since Matrix was in the game Recursive Canon kicked in and destabilized the game code. As Matrix derailed the game looking for the Number 1, the game code continued to deteriorate and all sense of logic was lost, resulting in a Mind Screw. Matrix's "chat" with young Enzo finally crashed the game and rendered Matrix unconscious while the User went back to playing a golf game. Being a game sprite AndrAIa's memory was reset when the ReBoot game crashed and had no idea why Matrix was unconscious, and decided to tease Matrix by saying he was knocked out by a golf ball.
  • AndrAIa wasn't teasing him, he actually had a lump on his forehead from where the ball hit him.

Daemon was the Y2K bug.
Think about it; a virus threatens the entire net and is going to cause the entire thing to crash, at a specific time. At the end of the day the virus disappears and no systems crash at all.

I can just picture the user being AVGN reviewing awful games. He could be complaining about The Computer Is a Cheating Bastard and Game Breaking Bugs. That also explains why he never plays the same game twice: he destroys the ones he thinks are bad

Hex isn't exactly dead

I mean, how can she make the closing narration if she's dead? In memory of Hexadecimal. Format - Virus: Savior of the Net.

Matrix's Eye can read sprite code
That's why he took an instant dislike to Ray Tracer. He was hope to stop him from meeting AndrAIa, since what he would do then was written all over his code.

There was no retcon of Bob's backstory
Just because he originally went to Mainframe earlier than we thought doesn't mean he stayed there. We saw the other Guardians show up shortly after he followed Kilobyte's signal. They likely cleaned up the damage caused by the explosion and took Bob back to the supercomputer to finish his training. Bob finished his training and went on to be a great Guardian, catching Mouse and earning himself a great reputation which in turn caused Turbo to grant him the opportunity to test his theory in Mainframe.
  • His deleted partner kept on refering to him as Cadet, so it's pretty obvious that he didn't stay in Mainframe.

Matrix spared Megabyte in Showdown because of the episode Talent Night.
Because in that episode, Megabyte gave Enzo a guitar for a birthday present. After rocking out with it for absolutely no reason other than "I've always wanted to do that". It was just barely redeeming enough to justify sparing Megabyte one time.

Mouse is the avatar of a User

If I recall correctly, Mouse was stated to be a hacker. And if we assume that Reboot terminology is consistent with real life terminology, that would make Mouse a true hacker. (leap of logic goes to Trinity from The Matrix before she woke up?) As a result, she IS a user and her appearance is merely an avatar to prevent the denizens of Mainframe from effectively looking at an Eldrich Abomination.
  • The disguise is nowhere near perfect. She has fangs, and her "hair" is red static.
  • Alternatively, she could be a program created by a user for the purposes of hacking. Said user could then have moved on to other programs or methods, leaving her to her own devices and allowing her to become autonomous.

Mouse is Mouse
Stemming from the above, Mouse in reboot could be an avatar of Mouse from The Matrix. It's already shown that he likes to program female characters.

The User in "Game Over" was using a cheat code

Take a look at that fighting game, and tell me that Zaytan wasn't the final boss. Which would make Enzo managing to go all three rounds against him at that time all the more impressive.
  • The Game is a reference to Mortal Kombat, and several of the games from that series have their final bosses as freely playable. Zaytan seems to be a reference to Satan, in Mortal Kombat Shinnok plays that role, he was playable as a regular character in his debut game and started things off by killing off a few heavenly characters. Perhaps unintentional but it fits pretty well.

Mouse is a Game Sprite
Let's look at the signs:
  • Very capable in physical combat, far beyond any other character except perhaps AndrAIa
  • Possesses extreme skills in specific areas far beyond any other character
  • Has physical traits not shared by any other character (her static hair and fangs)
  • Similar icon form to AndrAIa until she changes it
  • She was performing her skills with no clear motivation (hacking, etc.) or goal in mind and latched onto people she found as friends.
  • Never mentions actually being from anywhere and shows no surprise or distrust of AndrAIa

There were no backups of Mainframe or its sister city prior to the sister city's destruction
How do we know?
  • During the system restore at the end of season 3, the sister city was not restored, nor were its inhabitants. Further, the last remaining part of the sister city, Lost Angles, was also not restored.
  • It echoes Real Life: A surprisingly large number of computer users do not start using a backup system until they've already lost something important.

Bob wanted to reform Megabyte because viral infections last beyond the death of the virus.
There's a lot of callous behavior toward the viral binomes while Bob wanted to spare Megabyte. However, there might be a good reason: when virals lose their commander, they still try to live up to their standing orders. Megabyte's army would likely be in open revolt and try to exterminate their infector's killers. However, if Megabyte could be reformed, then they could cleanse Megabyte's army in short order.

Hex's gift hasn't completed its function

Null creature body and voice just isn't glorious enough to be all it did. When the time is right, little Enzo will go viral and save the day as a virus.

The Spectral System is a Mac

Note that the inhabitants are different from ordinary people often seen in the series (Spectrals instead of Sprite and Binomes) so the way that system operates isn't like the others. Then note that it isn't used games, so some of the inhabitants needed to go further than normal to adapt.

The thing about AndrAIa and bikes is:

She's an amphibious game sprite. There was probably a level in the game she came from where the User encounters her on land, and she's a biker babe there. Either that, or Mouse did it.

The Matrixes are from the Twin City

This is actually supported by the show, and a basic knowledge of binary. In Talent Night it's said to be Enzo's 1st birthday, but his shirt already reads "01" (1). Flashbacks in My Two Bobs show Enzo wearing a shirt with with "00" on it. He compiles to "10" (2) in the episode mentioned, and in season 3 Turbo mentions he should only be "11" (3). So it was Enzo's first birthday in Mainframe.

Hexadecimal will be resurrected at the next system restore

Because she was registered as a virus, she will return as a virus.

Gigabyte is more powerful than Daemon

Hexadecimal was an equal match for Daemon, and he has many useful powers that she lacks, such as generating portals. Gigabyte was only ever shown in a severely weakened state and with an energy parasite (the web creature) strapped to his back. At full power he was likely more dangerous than Daemon, at least 1 on 1, and if he ever got to full strength it might be impossible to stop him.
  • Hexadecimal was empowered empowered by the Core of Mainframe at the time. Granted, Gigabyte + Mainframe Core would probably wipe the floor with Daemon, though Daemon's powers seem more well purposed for massive widespread destruction than Gigabyte would be.

Megabyte had Little Enzo seized at the end of Reboot so that he could get at his icon
It was infected by Hexadecimal remember and if Trojan Horse Megabyte gets Hexadecimal's code he'll become Gigabyte giving him the power to perform The Hunt....
  • Does he even know about Hexadecimal's gift? Considering with his ability to infect multiple people at once (yes, the tentacles can be blocked), that just seems like overkill if he does. Not that he's beneath that or anything.

Megabyte created Daemon
He created a copy of Medusa and Bob had to go to the Super Computer to stop it. Megabyte could have created another Viral Bug and sent it into the Super Computer while Bob was entering it and programed it to infect Gaurdians and draw enough power to take a humanoid shape. Daemon did say she wasn't an entity...
  • Conversely the copy of Medusa is Daemon. Megabyte said Hexadecimal's Medusa is quite inferior to his so it's likely he designed it to infect Gaurdians and by the time its infection followed Bob into the Super Computer it mutated into Daemon and skipped the stone part and went straight to waiting until time runs out to delete everything(which Medusa does after turning things to stone: it waits for a time before it deletes the object).

Portals as magical plot devices...
Sometimes they just work like an Internet connection between two computers. Sometimes they can bypass any and all defenses and firewalls. There is a simple, logical explanation for this discrepancy: port numbers. Firewalls can be configured to leave certain ports open, generally for online games or other types of networking program. Similarly, some defenses may only cover the commonly used ports, leaving less exploitable ones open. It's possible that a portal can be configured to go through an open port, instead of being limited to the standard TCP/IP ports.

People from the Net will be able to enter the world of the Users when they are put into the minds of robots.
This will result in either a peaceful coexistence between the two races or a Robot War.

Mainframe is a computer in a video game company.
The real purpose of Mainframe is to test out new computer games made by the company.
The Real GhostbustersWMG/Western Animation (Series)Recess

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