Daemon continues to plan in order to retrieve Bob, who could help her infect the entire net. Matrix comes across a fully infected Turbo, and Hexadecimal experiences a certain change.
Matrix and Mouse plan to stop Daemon after AndrAIa is infected by her. Meanwhile, Dot tries to get Hexadecimal to bring back her father. Bob attempts to cure Turbo but his code doesn't work.
With Matrix, AndrAIa and Mouse converted, Daemon travels to Mainframe herself to complete her plans. Enzo finds himself the only one who can turn the tide, until Hexadecimal gets power from Mainframes core.
With the Daemon threat gone, a second Bob appears in Mainframe, leaving Dot with a difficult decision as to which one to marry. Meanwhile Matrix and "New Bob" deal with a game as "Glitch Bob" questions if he is in fact a copy.
"Glitch-Bob" thinks about separating Glitch from himself to return to his normal self. Matrix, AndrAIa, Enzo, Phong, and "New Bob" deal with a game that has a familiar User.
With "Glitch-Bob" incapacitated in the Supercomputer, Dot decides to marry the new Bob, but as "Glitch-Bob" regains his health and original form, the new arrival is revealed to be a disguised Megabyte.
With Megabyte now a shape-shifting Trojan horse virus, Bob, Dot and the others attempt to track him down and capture him. Megabyte tricks them and seizes control of the Principal Office, and swears revenge in the form of a Predatory Hunt.