After being given a sprite icon to thank her for her assistance in dealing with the collapse of Mainframe, Hexadecimal gets restored along the rest of the city when the user uses a backup image of Mainframe. Just like in real life, your viruses get restored if they were included in your system backup data!
Hexadecimal's attitude towards Bob makes a lot more sense when you consider that Kilobyte overheard his talk with Dixon before he upgraded. Hex knows Bob has no hostile intentions towards her so as long as he's not directly interfering in her plans she's perfectly happy to see him and even develops a crush on him, likely due to his own chaotic nature. Megabyte's behaviour also makes a lot of sense with this in mind, he knows Bob won't try to delete him unless he has to so his attempts to gain power are slow and subtle with the occasional grab at immense power, so Bob won't take extreme action until it's too late to stop him. Once Bob and the other Guardians were locked out of Mainframe he drops the subtle plans and goes all out.
After all these years it's only just occurred to me that Bob isn't Megabyte's foil, Dot is. Bob is Hexadecimals foil! Megabyte and Dot are both geniuses who plan and counter plan for control over Mainframe. Hex and Bob both fly by the seat of their pants and make things up as they go along. Both pairs also make excellent teams and are much less effective on their own! This is also why Mainframe wasn't completely screwed when they lost Bob, Megabyte had restrained Hexadecimal so the only threat they had to worry about was the one Dot was most suited to counter and she managed it perfectly until Hexadecimal broke free, interfered, and caught them all off guard.
In the Pantsu Hebi X game with Matrix and Bob, Bob gets pretty angry at Matrix and yells,"Matrix! stop trying to hit him and HIT HIM!" He then takes a moment to calm himself down. This seems a odd to hear from Bob. Then in the penultimate episode, we find out that this Bob is actually Megabyte pretending to be Bob.
When Matrix is infected by Daemon, Little Enzo has Frisket bite his hand to hold him in place. When Matrix begins to threaten Frisket, Little Enzo asks him if he will shoot the dog, something which happened in the first episode of season three when the user shot Frisket in an "Evil Dead" type of game, an event that made Enzo (who would later become Matrix) so upset, he had to be carried away from the injured Frisket by Dot. Surely the thought of shooting one's beloved dog would be hard for anyone to bear, but to consider the thought of shooting one's dog after the dog had already been shot once before, and to have been deeply upset by that past event, would certainly have a greater impact.
Matrix's interaction with "Bob" in the early parts of "My Two Bobs", as well as his strangely out of character hesitance to the idea of cheating and attacking the User running the overly-long-and-tedious game the two of them are stuck in , when he's previously done so before, actually makes sense when you remember a few things about Matrix's character; namely the fact that he's currently not on the best of terms with the original Bob, and the fact that he's struggling to re-integrate himself into Mainframe after a lifetime of fighting for survival. The show has expressed a few times that, deep down, Matrix is not happy with the person he's been forced to become, and that Bobs pacifistic-based criticism of the, sometimes justified, harsh methods that he's adapted to survive cuts him especially deeply, not to mention that his more violent approach to the Daemon War seems to have left something of a strain on their relationship. It's pretty likely that in the "My Two Bobs" episode he's trying to prove to "Bob", to Mainframe, and possibly to himself that he can play by the rules, and live normally in his now peaceful home, and is trying to gain the approval and respect of who the "clone" of Bob represents; the Sprite that Enzo looked up to as a role model, and whom he always wanted to impress.
ReBoot. When the User wins a game, a sector of the system is destroyed and anyone unfortunate enough to be there gets turned into little sluglike nulls. Now imagine Mainframe is that computer that you play your video games on all the time and always win.
Or for that matter, the game designers. Assuming their world is like ours, these things get play-tested; they know winning screws up the machine. Every game is Lose/Lose!
How AndrAIa came to be part of the show. In order to stay with Enzo outside of the game, she put a copy of herself on his PID that would leave with him. A COPY. This means that the AndrAIa we see throughout the series is really just a "clone", and that the "real" AndrAIa is still in the game, alone, without friends or her love. Now we know why she says goodbye just before the game ends...
This one gets even worse. Later its revealed that Games use Year Inside, Hour Outside, which gives Enzo a level in badass during a Time Skip. This means that the original AndrAIa aged faster than the copy. She probably died of old age before Season 4.
Or she got fragged by a user, considering a gamer's mindset when they shoot at things, she's probably like a goomba from Mario to most users. if the game doesn't simply restart like some real games. in which case, she's probably trapped in endless war with a user, without friends. forever.
Maybe this is why Wreck-It Ralph has the death outside your game is Permanent rule. Consider the episode AndrAIa: She attaches her Icon to Enzo's. While this is a backup, once the game ends, the original dies: with no icon, it has no data to restore her with. She removed herself from her Game's code. The arcade characters may have heard stories of the PC Game Sprite who ripped herself from her game's code. As Arcade characters they'd have no reason to know of backups in an adopted home system. A less horrible version is that it backed up her data on her Icon before it released her thinking she was Enzo (supported by the Wiki), but she still removed herself from her game's code.
What AndrAIa and Frisket did to the infected Guardians becomes Fridge Horror when you realize the Guardians weren't in control of their bodies, so they basically slaughtered and viciously mangled innocent people. Our heroes, ladies and gentlemen.
The alternative was to leave the infected Guardians to slaughter and mangle other innocent people, ones who weren't a threat. There's a trope for that.
AndrAIa is a Game Sprite. Killing things that attack her is her function, it's part of her code, she can't go against it.
Bob mentioned in his lecture on game sprites that there are Artificially Intelligent Game Sprites that can learn and adapt. Pretty sure AndrAIa can learn these sorts of things. Something I forget, though, is whether or not she knew about the infection at the time? Didn't Turbo only reveal it in secret?
Turbo was telling Matrix about the infection while AndrAIa took out the last of the Guardians hunting them. And while AndrAIa is an AI Game Sprite who will learn and adapt she still can't go against her code, nobody in the series can.
The issue of whether you can act outside your Code is a big debate in universe. Generally it seems to be assumed that you can't, but because Matrix, Bob, and Hexidecimal clearly did it's become less iron clad.
They never acted outside their Code. Their specific methods vary but they're always following the same goals that they always have. Granted, it's a bit unclear how much wiggle room they have due to free will and few characters really have their functions laid out for us but those that have are always consistent.
One thing that is clear is that code can be changed. Bob downloads his own code into Enzo's icon. Matrix's renegade stint, you could argue that he's still pursuing Guardian protocol, though with a bit too much fanaticism. Then again, we're back to the question of wiggle room on reaction to other programs.
AndrAIa's code seems flexible - or possibly her objectives. The majority of Sprites in her original game were supposed to attack anyone that held the intention of going after the treasure - AndrAIa launched Enzo at the treasure. That seems like a violation. Also worth noting that she did not attack her assailants in Where No Sprite has Gone Before either when the Spectres or the Sprites were going after her. However, her actions towards the Guardians does make sense. She doesn't learn about Daemon until after the battle as Turbo's only telling Matrix at the time but she did get the briefing from the Search Engine about a new Guardian regime and she encounters the Guardians after seeing the market they destroyed - a market she'd seen alive and bustling prior to their arrival.
During the System Crash Bob mentions "it goes against everything I am, but I'm not going into that game, you musn't either". His code compels him to go, but he knows that neither he nor Matrix should.
Live Null Juggling. There's a reason Dot says she thought it was banned. You're not juggling just any digital creature, you're juggling creatures that used to be people.
The Edge of Beyond. The most likely explanation for the massive tear in cyberspace is that it used to be a system like Mainframe that got torn apart by the Web or destroyed by the Guardian Collective.