Megabyte, now able to shift form, rampages through mainframe, but Bob insists his theories on turning a virus good will work.

The citizens of Mainframe start to battle the supervirus Daemon who has infected 92% of the Net. Bob is horrified to discover that she has infected all the other guardians.

The battle against Daemon continues, Hexadecimal turns into a sprite, we learn more of the character's pasts, the nulls form an old friend, and Turbo has been infected by Daemon.

Daemon finally infects all of Mainframe except for Little Enzo, Hack, Slash, and Frisket, who were in a game cube. Hexadecimal makes the ultimate sacrifice.

Dot prepares for her wedding with Normal Bob, Glitch Bob remains comatose in the super computer, and Glitch finally reveals the identity of the real Bob.

Daemon continues to infect more and more citizens of Mainframe, we discover more about Bob's past and his first coming to Mainframe, Bob's condition worsens, and Daemon learns about love.

While most of the gang battle Rocky The Rabid Raccoon in a game, Glitch Bob struggles to find a way to separate himself from glitch, and Dot follows her heart.

The two Bobs try to figure out which is the original and which is the copy. Dot can't decide which one to choose. A game cube drops placing Matrix, Frisket, and Normal Bob into a Pokémon style game.