When the Web invaded Mainframe, Bob had to rely on the computer viruses to build some hardware to close the portal. But right before the portal was shut, Megabyte betrayed Bob, threw him into a small rocket and shot him into the Web.

After, Bob was trapped in the Web, he met some sprites that had ended up there too (they were kind of degraded by the thick information of the web) , and he was chosen as their leader.

Later, Matrix, AndrAIa and Frisket rescued him from the Web with the help of the Crimson Binome, the crew of the Saucy Mare and a Web Surfer, Ray Tracer.

When they got to the Web address of Mainframe, the Saucy Mare that was covered in dead web creatures, triggered a defense mechainism programed by Mouse. The crew had no way of breaking through it, but Glitch "told" Bob that if he, Glitch, downloaded himself to Bob, they would be able to make it and not be deleted. Bob wasn't as sure of the idea as Glitch was, but when Glitch did download, Bob became Glitch-Bob and he got this really cool suit. (I think it's makes him look too thin!) Bob broke the web-creature shield, created portal to Mainframe out of the tear and transported all of them safely to Mainframe.

During the system crash, Bob had to go into the core and shutdown all the sectors of Mainframe.