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Bob did not come from Mainframe. Bob came to Mainframe following the virus that deleted his colleague.

From what we know, Bob was a cadet in the Super Computer training to become a guardian at the academy. Bob, and his colleague named Dixon Green, were discussing Bob's theories while getting a virus named Kilobyte ready for deletion.

Unfortunately, Kilobyte broke free and began to upgrade. Bob attempted to rescue his partner, but was effortlessly thrown to the side. Dixon called for help using her key tool, Glitch, but it was too late. She attempted to stop the virus, but in the process, the virus attacked her and she started to disappear.

Bob began to regain consciousness just as the virus escaped into a portal.

(Later, we learn that this was the same portal created by Dot's father, Professor Matrix. Kilobyte upgraded to Gigabyte and came through this portal. This caused the portal experiment of Professor Matrix's to fail. And this lead to the Twin City Explosion - the deletion of a twin city to Mainframe located directly next to it. Luckily, Dot and Enzo were on the other city at the time and were not deleted. However, tears appeared all over Mainframe and the city was heavily damaged. This explosion also gave birth to Hexadecimal and Megabyte. Now, back to Bob...)

Bob ran to Dixon's side just as she began to fade away. Her key tool, Glitch, began to remove its code from the dying guardian. Bob began to cry and yelled at Glitch to stop. Glitch completed its process and removed itself from Dixon. Dixon then looked into Bob's tear-filled eyes and said her final words. She died in Bob's arms.

"NOOOOOOO!"

As Bob cried, Dixon's key tool came to him. It found him to be a wonderful partner and attached itself to his wrist. Glitch then exchanged code with the cadet. Bob realized that he and Glitch were now partners.

Bob pulled himself together and created a portal to follow the virus that deleted his friend. He found himself in the system known as Mainframe. All around him was a system that seemed to be in a state of disaster.

The young guardian quickly spotted tears and began to mend them. Behind him, he heard a voice, and turned to see a young green sprite holding her younger brother. She asked him who he was. Bob introduced himself as a guardian and explained that he came from another system known as the Super Computer.

The green sprite was Dot - a young girl that had just lost her father. She blamed Bob and slammed her fists on Bob's chest. Bob explained to her that he did not cause all this and that he was here to help. Young Dot broke down in his arms.

Afterwards, Turbo and other high-ranking guardians came through a portal and met with Bob.

Bob now had a keytool and was trained enough to be a full guardian. Turbo allowed Bob to become the guardian of the system with the newly arrived viruses - Mainframe.

Bob had lost his colleague. He, however, had gained Glitch - his key tool that would follow him to the end. He now had a system to mend and defend.

And that's how Bob became the guardian of Mainframe.