Yeah, they found Bob with the Web Riders. He was all warped and crazy looking thanks to whatever the Web does to sprites, but otherwise he was the same. They ended up going back to Mainframe and he merged with Glitch so that the Saucy Mare could penetrate the firewall and get back into the system.
The last part of the season was basically everybody back in a ruined Mainframe trying to take it back from Megabyte (who got control of the place in the absence of Enzo and Bob). At the end Matrix managed to take out Megabyte, but as he died he started crashing the system. The last system was a little apocalypse scene, and then the User rebooted Mainframe and everything was back to normal.
The whole last half or so of the first three seasons was summed up at the end in a nice little Opera
At the end, basically everything was the same except that (since Matrix's icon was altered when he left Mainframe) there was a young Enzo and then the grown-up Matrix, Bob was still merged with Glitch, and Hexadecimal was reformed into a harmless good character.
Some time after the end of the third season there was more produced that was either a short fourth season or a series of OVAs, depending on how you look at it. The first of those was a storyline that brings closure to the story with Daemon (a supervirus that was infecting the Guardians along with the whole Net). It was actually pretty entertaining, and has some cool stuff in it (Mike the TV getting infected and turning into a televangelist, and Hexadecimal absorbing Mainframe's Core and then beating Daemon down hard, reverting back into a virus form). The second one was a more lighthearted story, about a second Bob showing up out of a portal. He looked like Bob did pre-Web Riders, and it was about Dot having to decide between the two of them, and also a lot of backstory like the accident that produced Lost Angles and the Origin of Bob/MegaByte/Hexadecimal and how Bob came to Mainframe.
It had a twist ending that basically allowed the entire show to return to the way it was at the beginning, with just a few changes.
Nothing else has been made since then, and the chances of getting anymore ReBoot is probably pretty low.