The main antagonist of the series, Megabyte (voiced by Tony Jay) is a virus, originally operating out of the Silicon Tor in Sector 1000 and dominating most of G-Prime. Megabyte plots constantly to corrupt and control Mainframe in order to turn it into his own domain, "Megaframe", and from there infect the Super-Computer and then take the entire Net. His secondary objective is to destroy his sister Hexadecimal, which is apparently just viral sibling rivalry. He is a malignant virus able to infect other programs, and commands an army of infected Viral Binomes. He has a brutal, almost psychopathic nature and speaks with a deep British accent. Megabyte possesses fantastic physical strength, super agility and reflexes as well as the ability to jump great distances. He can quickly scale high walls with vicious Wolverine-like extendable claws on his knuckles, as well as finger tips with extending nails similar to Lady Deathstrike. He has an exceedingly cunning intellect as well as the ability to infect and control objects. Another ability he has shown is the ability to read memory from certain sprites, namely Phong (Infected). He also manages to steal Bob's exchanged Guardian code with Glitch. Megabyte has no sense of morality and consistently takes advantage of others to achieve his own ends. He also seems immune to the energy-draining effect of nulls (as he has been seen holding his pet null "Nibbles", whom he once called "Father"). Megabyte can also store codes to control programs and functions of what ever system he is in, provided he has been given said codes. These programs are controlled by buttons located under a panel in his right arm. Megabyte also has a sense of humor and musical talents, as shown in the episode "Talent Night" when he crashed into Enzo's birthday party, accompanied by armed guards, but instead of his usual evil antics, he began to play a rock song on a forked guitar, which led to his and Bob's famous rock duel. Afterwards, Megabyte remarked "I've always wanted to do that", and left, but not before giving Enzo his guitar as a birthday gift. Megabyte's origin is revealed in the fourth season. He and Hexadecimal were once one virus (Killabyte), who was scheduled for deletion by the Guardians, but upgraded into Gigabyte before it could be carried out. He mortally wounded Bob's partner and moved in toward Bob before being accidentally teleported away by Welman Matrix's gateway device. The results were devastating: the destruction of Mainframe's twin city (creating Lost Angles), everyone present being nullified (including Welman, who became Nibbles), and Gigabyte being split into Megabyte and Hexadecimal. Upon being separated, Megabyte observed his surroundings and walked off – intent to carry out his agenda on an unsuspecting city. While always a villain, in earlier episodes Megabyte was often involved in humorous situations and rarely caused permanent damage; the exception to this was the first episode, "The Tearing", where he deliberately causes a whole Sector to be nullified. As time went on, and especially after ReBoot was no longer on the ABC Network, he became far more evil. He appears to have some small sense of honor, shown in one instance when Bob saves his life, Megabyte later let Dot go in the same episode, after which he commented "Now, we are even". In the final episode of Season 2, Megabyte worked with Mainframe to close the Web portal that had opened in Mainframe, but not without heavy cost. Unfortunately, just before his "hardware" was fired at the portal to close it, he threw Bob into a rocket and sent it soaring into the portal. The portal was then closed, and he had his army move to crush the remaining defenders (CPUs) of Mainframe. For the first three episodes of Season 3 he had complete air supremacy and full run of Mainframe, while its defenders were trapped in the Principal Office. He also left Enzo alive so he could launch a propaganda campaign focusing on how the Guardian was an inexperienced boy, thus demoralizing the denizens of Mainframe. Obscenely, he also imprisoned Hexadecimal and forced her into becoming a living weapon, electrocuting her viciously via a collar at the slightest whim. "Rather good, isn't it?", he remarked to Enzo about his latest "weapon". He was finally trapped behind an inverted Firewall that covered all of G-Prime. Unfortunately, shortly afterwards a rampaging Hexadecimal took out the Firewall; resulting in war between the viruses that devastated G-Prime (including the Tor) and neighboring Sectors. Needing a new base, and as the Principal Office shields were still offline (having been deactivated to provide energy for the Firewall) Megabyte was able to conquer it by force. Mainframe became Megabyte's long sought after Megaframe. Instead of re-building it "in his own image" (as he so frequently says), he more left it as a decaying and devastated system that was perpetually on the verge of crashing. When Matrix and Bob returned to the system, Mainframe's rebels were finally able to bring down the Viral forces. During the battle, Megabyte was confronted by Matrix, who was carrying his sidearm: Gun. Megabyte convinced Matrix to drop his weapon and fight him hand-to-hand, as the virus believed that "the boy" would be no match for him physically. However, this was proven to be false when Matrix ultimately defeated him in battle. Megabyte was enraged when Matrix spared his life, and as an act of desperation he tried to escape to the Super-Computer. However, Mouse managed to change the address of the portal Megabyte was using, and as a result he was trapped in the Web. He made a brief return in the form of a holographic simulation, which Megabyte had created to taunt anyone who went into the System's Core to prevent it from crashing. Megabyte survived in the Web due to sharing some of Bob's Guardian code, and in the fourth season he became a Trojan Horse virus, gaining the ability to look and sound like any sprite or binome he is able to steal code from. He returned from the Web in the form of Bob circa Seasons 1-2, deliberately trying to confuse everyone over who the real Bob was in order to attack his enemies emotionally. He had also switched objectives from world conquest to personal revenge. His plan worked so well, he almost ended up married to Dot, until Glitch retook Bob's stolen code and forced him back into his Viral form. Megabyte immediately fought the real Bob, but he was surprised by Bob's increased power and was forced to retreat. Afterwards, Megabyte began building an army of Neo-Virals, but was swiftly captured by the CPUs along with his whole horde, or so everyone thought. That Megabyte was in fact an alias, a fragile copy of himself, while the real Megabyte had infiltrated the Principal Office in the form of Frisket. He swiftly infected the War Room and had his enemies isolated throughout the building, telling them to prepare for "the Hunt". At the start of the Code of Honor webcomic, he'd devastated Mainframe with his armies of infected "zombinomes" that the entire System was evacuated. He was seemingly killed when the firmware upgrade Gnosis was unleashed on Mainframe,[6] but the second issue ended with him revealed still alive and working for Gnosis as an avatar created from Gnosis. Megabyte has an unusual habit of separating his torso from his legs when he is plotting at the Tor, and has a hovering chair to move him around when in this state. He has been in Games five times, showing the ability to infect the User's in-game avatar. His last two Games were played when he was disguised as Bob; he was able to reboot and handled the Games quite well, though he asked Matrix to cheat in Panzu Heavy X (My Two Bobs) when panicked about the number of opponents. His Game appearance in "Bad Bob", when a corrupted Game merged him with and a device stealing the Core energy, was the Megatruck. Bob drove him in this episode, and was alarmed to discover the Megatruck had no brakes. His name is a reference to a megabyte.

Community content is available under CC-BY-SA unless otherwise noted.