It didn't end.
At the end of Season 2, Bob got shot into the Web by MegaByte, leaving only Enzo (now a rookie Guardian) and the others to take care of Mainframe.
After getting kicked around for a while, Enzo (along with Andraia and Frisket) got trapped in the Net in Season 3. After growing into a majorly cool badass renegade (Andraia grew into a hot babe), Enzo made his way over to the Web, rescued Bob, made his way back to Mainframe, kicked MegaByte's butt, and MegaByte got trapped in the Web like Bob was.
Then in the first half of Season 4 (season 4 is made of two movies), Glitch-Bob led Mainframe in a battle against the Guardians, who had all been corrupted by a super-virus named Daemon, and Mainframe eventually won thanks to Hexadecimal.
In the second half of Season 4, the Surfer found another Bob in the Web, and while Mainframe was trying to figure out which one was the real one and which one was the copy, MegaByte came back, even stronger than before, took over the Principal office, and said that he was tired of playing games and now he just wanted to hunt down and kill everyone in Mainframe. End of Season 4.
There is no Season 5, and there likely will never be one.