A supervirus known as Daemon has taken over the Super Computer, and is trying to infect the entire net. Despite being a virus, she is not malevolent, and only wants to bring order to the net. To this end, she used something called 'The Word' to brainwash people she comes into contact with, and has already infected all of the Guardian Collective, apart from Bob and Matrix.

At the end of Daemon Rising, Bob and Dot got engaged. To the confusion of everyone, however, a portal opens from the net and Ray Tracer and another Bob steps through. Inasmuch as the second Bob looks like the original from Seasons 1 and 2, Dot names the Bob which merged with his keytool Glitch Bob. Most of My Two Bobs is taken up with the efforts of Dot, the two Bobs themselves, and the other mainframers to ascertain who is the original and who is the copy and in general to come to terms with the situation.