The mysterious sprite gunslinger called Nil Cipher hails from the lost system of BIOS, where he grew up with his brother Void.  The two brothers were inseparable, both wickedly skilled with the sharpshooting games at their local arcade.  Nil's life changed, however, when a wounded Codemaster fell into BIOS.  The Command.com helped the Codemaster recover, and during his convalescence, he befriended the two brothers.  Recognizing their skill, he offered to take one of the two off for training.  Nil won the lot drawing and said goodbye to his friends and family.  He trained to be the best gunslinger in the Net, and with his uncanny speed earned the monkier the 'Never Idle Sprite.'

Then Cipher received word that two virus siblings named Michel Angelo and Melissa had invaded BIOS and destroyed it.  Furious, the gunslinger hunted down any virus he saw, but then the Guardians were Infected by Daemon.  Now distrustful of the Guardians as well, Cipher attacked them as well.  This earned him the ire of Guardian Ranios, who hunted down Cipher and attempted to delete him.  The gunslinger escaped however, dealing Ranios a near-fatal gunshot wound to his right eye.  The Guardians damaged Cipher's custom-designed hoverfighter, Car, forcing Cipher to crash land in Mainframe.

Unfortunately, Cipher and the Mainframers did not get off on the right foot.  He attacked Bob, Matrix, and the amnesiac RAM, then the semi-benign virus Hexadecimal.  It took a Game from the User to force them to make a truce, and following the Game's end, Cipher decided he could trust the Mainframers.  He apologized for his attacks and the damage Car had caused during its crash.

All was not well, however, as Michel Angelo and Melissa on their flagship, the SS Mitnick, came to Mainframe looking for the Cybernomicon, a mystical artifact that would allow them to usurp Daemon's throne.  With much of Mainframe's elite captured, Cipher was forced to ally with Hexadecimal and Little Enzo Matrix to break into the virus-controlled Principal Office and fight off his sworn enemies.  Soon thereafter, the Cybernomicon was located, prompting another viral invasion.  Cipher attacked Angelo, and with the help of the restored RAM (or Pentium) destroyed the virus forever.

Cipher, with his repaired Car, returned to the Server with Pentium to help him in his mission to destroy Daemon -- though Cipher largely tagged along because he knew Melissa would covet the Cybernomicon, and he still wished to destroy her.