"New sprite in town" guardian Bob is having more than his fair share of problems when virus Megabyte threatens his new friends unless he completes a mysterious favour. Backed by his friends Bob refuses to comply but it's not long before the whole city is under threat from Megabyte's army leaving Bob with some tough decisions.

Enzo is doing his own delivery service at his sister's diner. Only he hasn't received any deliveries so far. Things seem hopeless for him until Megabyte's Vid Window comes up on line telling Enzo that he has a package that needs to be delivered to Hexadecimal, a multi-mask wearing virus who lives at the scarce location of Los Angles. Knowing Megabyte to be bad news in all, but Enzo couldn't resist in doing a single delivery order. He didn't tell Dot or Bob on who sent the package, but both Dot and Bob agree that it's too dangerous for a Sprite like Enzo to deliver a package in Los Angles, so Dot insists that Bob delivers it. The package in fact is a mask shape time bomb that will delete whoever is in possession of it. Hexadecimal is aware of this and puts the mask on Bob and sends him flying back to Mainframe. Enzo heard the news, then told Dot, and they now need to warn Bob about the mask he has right now. But a Game Cube is being inputted and Bob heads for the landing site for the Cube. Dot and Enzo followed him and made it inside the game which is a Racing Game. But will they manage to tell Bob to get away from the mask before time runs out?

Slow Food doesn't come fast like Fast Food.

When Hexadecimal tricks Megabyte into releasing the Medusa, an unstoppable viral bug, on Mainframe, it's up to Bob to save the day.

Bob and Dot brake up.

Unformat Command isn't edible.

Mainframe is raided by Captain Capacitor and his crew of software pirates. When Bob is captured and thrown in the brig of the Saucy Mare, 'Admiral' Dot must give chase and save the day with some fancy (mostly verbal) fencing.

In an attempt to make himself smarter, Enzo inadvertently turns everyone in Mainframe into simple dolts. Now he must turn them back to normal before their naive ways get them nullified in a Track and Field game.

Bob, Dot and Enzo are stuck in a role-playing game with the intrusive Mike the TV.

In an attempt to access the Supercomputer, Megabyte hires a hacker named Mouse to enter Bob's brain.

Dot prepares a surprise talent show for Enzo's birthday; Megabyte, upset about not being invited, prepares his own act.

Dot has to convince a sector under Megabyte's control to give her their PID codes in order to convert their sector back to its normal state.

After being betrayed by Cyrus, Dot's emotions of guilt get the better of her during a difficult game.

Disguised as an upgrade, Megabyte enters Mainframe's core control chamber. He badly wounds Phong and initiates an Erase Command that almost destroys the System, only to be thwarted by Bob exploiting his greed. This is also the episode where we first find out that Megabyte is related to Hexadecimal. Hexadecimal (to Megabyte)" Now, you wouldn't be intending to erase me? Would you?" Megabyte (replying to Hexadecimal) " Oh, come now, would that be any way to treat...family?"

A Codemaster, Lens the Reaper, wreaks havoc in Mainframe while looking to challenge the legendary Codemaster Talon who took refuge in the system. Phong and Bob assure him that there is no one in Mainframe called Talon. Enzo discovers that Old Man Pearson is Talon, and has to convince him to come out of hiding—while Bob tricks Lens into a Game with the hope of nullifying them both to save the System. In the end, Lens is moved by the Mainframers' willingness to die for each other.

Megabyte uses game energy to break into Mainframe's archives. He causes two games to merge into one and becomes trapped in the game himself. Bob unwillingly saves his life, forcing Megabyte to grudgingly let him go when he captures him in the archives.

Megabyte attacks the Principal Office to steal Mainframe's Core energy. This causes a Game to be corrupted and land on the Principal Office. Bob and Enzo have to get the Core energy—being transported by "Megatruck", a transformed Megabyte—back to the Office before it can leave with the Game.

Hexadecimal accesses the system's Paint program, and Mainframe is her canvas. She soon begins to wreak havoc, causing a communications blackout, and melting all forms of transport. She also humiliates Megabyte. This is the first episode of a story arc that lasts for the rest of the series.

Enzo is angry because he feels lonely. During an underwater game, he unintentionally befriends a game sprite named AndrAIa. When the game is won, he discovers she attached a back-up copy of herself to his icon so they can remain together.

A Web Creature infects Hexadecimal. In order to protect Mainframe from her, thousands of nulls cover her, including Megabyte's pet null, Nibbles (who is, in fact, his nullified father). Hack and Slash, Megabyte's assistants, were babysitting Nibbles at the time, and rush to find him. They collide with Bob, Dot and Enzo. Phong dresses up the group in Power Ranger-like uniforms, and their vehicles form a giant robot and battle the monster, dubbed Nullzilla by Mike the T.V. Eventually, however, it is AndrAIa who saves the day. Hexadecimal is back to normal, but the episode ends with the Web Creature attacking Megabyte.

The possessed Megabyte merges with Hexadecimal, creating the terrifying energy-absorbing virus, Gigabyte. The Mainframers fight to stop him gaining full strength, alongside both Hack & Slash and a returning Mouse, who is initially disliked by Dot, but the two are forced to work as a team and sort out their differences in the battle against the new virus.

Mainframe citizens are mysteriously disappearing, including Dot and Al's waiter. Phong hires two CGI Special Agents, Fax Modem and Data Nully to investigate the disappearances, along with Bob and Mouse.

A portal to the Web hovers over Mainframe, and its citizens must prepare for war. Megabyte and Hexadecimal join the battle, but they have a secret ulterior motive.