A tear is opens in Mainframe (The computer city the show is set in) and Megabyte (A Virus) plans to use it to access the Supercomputer. Only two things can stabilize a tear into a portal: A Guardian or a game. Megabyte tries to strike a deal with Bob (The city Guardian), to stabilize the tear, allowing Megabyte to lead his army to infiltrate the Supercomputer. Bob refuses to cooperate and manages to escape, but then a game cube descends. The game is an outer space spaceship simulator. Megabyte, Bob, and Dot (The heroine of the show) enter the game, where MB infects the user and takes control, heading for the tear which has now become a portal. It's up to Bob and Dot to stop him.
When Enzo opens a delivery service, Megabyte find opportunity to plan an attack on Hexadecimal. Megabyte sends Enzo with a package in which on his way to deliver, Bob takes the package and delivers it for him to keep him safe. Hexadecimal knew it was a bomb, and tells him to take it back, but Bob is now in danger of the bomb.
Bob tries to save Dot before she is erased.
When Megabyte steals Hexadecimal's Medusa Bug, he discovers it was a trap, and turns everything to stone. Bob happens to be untouchable of the bug and must get Hexadecimal to return Mainframe to normal.
Frisket eats an unformat command belonging to Megabyte, so Megabyte kidnaps Enzo as a way to capture Frisket.
When Dot is late to an appointment due to Bob she starts to think he is too childish and she is too up-tight. Enzo and some help of the other sprites and binomes, tries to help them make up.
Mainframe is attacked by Software Pirates that steal everything of value and it's up to Dot to save the day.
Enzo gets his wish to be smarter than everyone when the Master Clock slows down and makes everyone else dumb.
Mike the TV is driving everyone crazy but when a Game cube drops, it's up to Bob, Dot, Enzo and Mike to stop the user in a Dungeons & Dragons type game.
Megabyte intends to send a heavily compressed ship inside Bob's brain but fails when it ends up inside Enzo. Now Bob has to take a fantasy voyage inside Enzo with the help of hired mercenary, Mouse.
Dot and Bob have a surprise birthday party planned for Enzo. Dot arranges the acts while Bob keeps Enzo occupied, but Megabyte wants to make a surprise appearance.
Dot tries to make things better for the binomes in one of Megabytes sectors to entrusting her with their PIDs. But when virals attack the meeting place and their PIDs are stolen.
Dot gets to see how important she is to Mainframe, when Phong sends her to the future where Bob would be reduced to a Null, and Megabyte would take over Mainframe.
When Mainframe gets a system upgrade, Megabyte gets into the Principal Office and goes directly for the Core.
A mercenary Codemaster has come looking for another member of his guild.
Megabyte starts draining energy from the games to break into the Archives. But when Hack and Slash drain too much energy from one cube, the game crashes and resulting in the User downloading a second game on top of the first, trapping Megabyte and Bob inside.
Megabytes meddling with the Core energy causes a game cube to be corrupt and now it's up Bob to keep the game going until he can get the energy back to the Principal Office or Mainframe will shut down when game ends.
Hexadecimal manages to tap into the system's paint function, causing Mainframe to become a gallery of her works.
Enzo, is all alone. He is the only young sprite in Mainframe. So when he enters a game, against Dot's rules, he meets a game sprite named AndrAIa.
Mike accidentally shatters Hexadecimal's looking glass and a mysterious black fractal creature comes out of the Web and attacks Hexadecimal. All the nulls cover her forming Nullzilla.
Megabyte merges with Hexadecimal to form a much more powerful super-virus: Gigabyte.
Phong hires two agents to investigate the Web creature and see what Mouse has to do with it. But when Dot disappears, Bob gets involved.
The very existence of Mainframe is at stake and out heroes must rely on Megabyte and Hexadecimal for help.
Megabyte and Hexadecimal turn against their temporary allies and try to take over Mainframe. But with Bob gone it's up to Enzo to save Mainframe.
Megabyte's propaganda campaign is turning Mainframe against Enzo. Enzo takes a stand as a guardian and enters a Game Cube without Dot and must battle the menace of 'Rocky' - the Rabid Raccoon.
Megabyte plans the final onslaught against the Principal Office, but Enzo and AndrAIa must prove that Enzo is a true Guardian. Meanwhile, Dot and Mouse try to stop Megabyte.
Enzo and AndrAIa enter a game alone. Enzo tries to win to prove he can do anything. But can he win?
Enzo and AndrAIa are now all grown up and have been moving from system to system through the games for a very long time, searching for a way back to Mainframe. They find a system in need of repair and train a few binomes to help the system for any future games.
Matrix and AndrAIa are on different sides of an arguement when they arrive in a system filled with Superhero Sprites and Spectrols.
Matrix and AndrAIa reboot into what seems to be Mainframe, but Dot, Phong and Bob are acting out of character. But he and AndrAIa reboot as Megabyte and Hexadecimal!
Matrix and AndrAIa find a system with ports to the Net but renegade Guardians have taken the system under siege.
Matrix and AndrAIa meet up with Captain Capacitor who was thrown into jail by the Guardians. The Captain promises Matrix that he'll help them find Bob as long as he and AndrAIa break him and his crew out of jail.
Tensions mount between Matrix and Ray Tracer, but they have to work together when the ship's portal generator breaks down. When a web creature bites AndrAIa draining her from half of energy, Matrix is determined to save her.
The Saucy Mare is attacked by people riding the Web creatures but a sprite calls off his crew and AndrAIa is saved by an old friend.
Traps left by Mouse to keep web creatures out of Mainframe, stop the heroes from getting home.
Bob and Matrix return to Mainframe, to see it devastated. Hexadecimal and Megabyte have gotten out of the firewall and taken over.
The battle for Mainframe begins, Megabyte and Matrix have a final confrontation. While Bob has to deal with Hexadecimal.
The whole system starts to shut down and Users game sprites are run rapid throughout the city.
Mainframe is doomed, but Bob convinces Enzo to let a Game Cube finish off the city with the hope that the fate of Mainframe is in The User.
Mainframe starts to battle the super-virus Daemon who has infected most of the net and all the other guardians. Knowing that he is the only one left, Bob is horrified.
The battle against Daemon continues, we learn about of Dot's past, Matrix learns more on Daemon and Hexadecimal is turned into a sprite.
Daemon continues to infect more citizens of Mainframe and we learn about Bob's past.
Daemon has infected all of Mainframe, except for Little Enzo, Hack, Slash and Frisket. With all the major combatants infected, who will save them?
When a second Bob comes into Mainframe, no one knows which is which - including the two Bobs. With the wedding preparations underway, Dot can't decide who to marry and turns to her friends for assistance. Will the real Bob please step forward?
Matrix, Enzo, AndrAIa, Bob 2, Phong, Hack and Slash battle Rocky the Rabid Raccoon in a Star Wars type game. While, Glitch-Bob tries to separate himself from glitch.
The wedding day draws near, but while preparations are being made for the nuptials, Glitch-Bob is still in some sort of strange coma after having attempted to try and separate himself from Glitch. Can he awaken in time to tell Dot how much he loves her and prevent the wedding from going ahead?
With the true identity of Bob 2, the people of Mainframe are in panic. Megabyte, a Trojan Virus that can shape shift, is now raging through Mainframe, but Bob believes that his theory on turning a virus good will work.