- "You have no defenses you fools, your Guardian is lost! Nothing can stand in our way. Mainframe is ours." -Megabyte
The First War
Following immediately on from the Web War and the loss of Bob, Megabyte launched a surprise attack on the worn CPU fleet. By the end of the fight, all but nine of the ships were shot down, leaving Megabyte with complete air supremacy.
The Hardware used to close the Web Portal was recharged to fire at the Principal Office. Hexadecimal damaged the buildings shields enough that they were on the verge of collapse. The remaining CPU fighters requested landing clearance as the ABCs chased them toward the Principal Office. Dot ordered them to fly to the Principal Office single file. They did so, and the ABCs came at them in a cross fire formation. Just as they targeted the CPUs, the Principal Office opened fire with its Anti-Aircraft Guns. The ABCs were destroyed and the CPUs saved, but one damaged ABC crashed into the Principal Office, damaging the shield generators.
With the Principal Office defences down, Megabyte told Hexadecimal to power down. With Hexadecimal still willing to destroy the Principal Office, he explained the destruction of the Core would destroy the entire system and them along with it. Ignoring his warning, Hexadecimal prepared to fire. Megabyte tried to stop her but Hexadecimal threw him aside and charged the Hardware again. Just as she was ready to fire a Game Cube began to land and came down on the front of the Hardware. The device overloaded and fed the Game energy and its energy back into Hexadecimal. The Hardware exploded and nearly deleted Hexadecimal.
After repairs were made, the Principal Office was forced to raise its shields, cutting it off from the rest of the System, and could only send the occasional mission, mainly to handle Game Cubes. Megabyte was effectively allowed free reign. (Between a Raccoon and a Hard Place)
Mainframe struck a winning blow to Megabyte with a new development in Firewall technology. Phong and Mouse designed an "Inverted Firewall" that could seal off Giedi Prime from the rest of the city. The sudden strike left Megabyte and his armies trapped, ending his threat in one swoop. A large number of anti-aircraft guns facing G-Prime would repulse any breach of the Firewall, seemingly ending the threat. (Firewall)
Megabyte forced Hexadecimal to use her viral powers to breach the firewall. She initially refused, but agreed when he threatened to turn on the pain collar. Hex opened a small opening in the firewall large enough for an ABC to pass through. Megabyte ordered Lieutenant Chauncy to lead the ABC attack fleet and seize the Principal Office.
As the ABCs emerged from the firewall, Dot waited for Megabyte to follow his forces. Phong told her they couldn't wait and they ordered the Anti-Aircraft Guns to open fire. They managed to destroy the ABCs that came through and some shots made it through the rift in the firewall. Megabyte realised their mistake and ordered the rift closed. Hexadecimal laughed at him and let the rift close. The remaining ABCs attempted to return to the Giedi Prime, but collided with the firewall as the breach closed.
Megabyte put Hexadecimal back in her cell, and ordered Herr Doktor to begin work on their own firewall disruptor. The first war came to a close with this failed attack. The last blow to Mainframe was the loss of Enzo Matrix and AndrAIa in a Game Cube. (Game Over)
The Second War
The second war began when Hexadecimal broke free of Megabyte's control. In the first few moments, she destroyed Silicon Tor and overloaded the Firewall that kept the Viruses contained. The resulting battle pitched Hexadecimal & hordes of Nulls against Megabyte's entire army and saw the G-Prime Sectors devastated with the ABC's taking heavy losses. As Megabyte and his army were still alive at the end and Hexadecimal had returned to Lost Angles, its most likely Hex got bored with the fight and returned to Lost Angles.
The second battle of the Viral Wars began when Megabyte, needing a new base, launched an all-out assault on the Principal Office. The attack would appear to have come from a different sector to G-Prime, as only two minor anti-aircraft guns were shown standing against them. Megabyte's overwhelming barrage forced Phong to evacuate the Office, leaving it in viral hands. Phong told Dot Matrix to lead their forces to safety and stayed behind to delay Megabyte. When the virus arrived he decapitated Phong and kept his head so he could extract the city command codes from his mind.
Following this battle, Megabyte spent the rest of the Viral Wars in full command of the city, renaming it Megaframe. The CPU forces worked as a resistance unit for the rest of the war. A combination of battles between Megabyte's viral army and the Mainframe Rebellion, lost Games and viral takeover caused the System to gradually collapse, to the point where every Sector had been destroyed and Tears went unfixed. The length of the Viral Wars are unknown, as are any actions taken by Hexadecimal during them. (Megaframe)
Megabyte realized the system was back on the Net and prepared to leave the dead city. He forcibly extracted portal command codes from Phong so that he could create a portal to the Super Computer. Phong tried to fight against Megabyte, but eventually failed. As they finished extracting the first set of codes from Phongs mind, the Sub-Sphere exploded, releasing a tear capable of forming into a portal to the Super Computer.
The Wars ended with the return of Matrix, AndrAIa, Bob and the Saucy Mare to Megaframe. With the Mare, Dot was finally able to carry out a plan to cripple the ABC fleet. They sent the Saucy Mare with no crew and filled with explosives slowly moving toward the ABC fleet. The ABC pilots deliberately allowed to get close so they could all shoot it down. The ship exploded and destroyed all the remaining ABC fleet, and the remains of the Saucy Mare crashed into the Energy Sea.
With viral air cover gone, the Mainframe Rebellion was able to mount a ground assault to retake the Principal Office, while Matrix took down Megabyte.
Megabyte nearly escaped the system through his portal to the Super Computer. Mouse managed to hack into the portal and change its destination. As Megabyte stepped into it, the portal changed to a Web portal, and several Web Creatures pulled him into the Web.
Hexadecimal was finally removed as a threat when Bob repaired her cracked mask. She was actually able to move her mouth without changing masks. She completely switched sides, sending Bob back to Dot. (Showdown)
Megabyte latter returned in the form of a Trojan horse virus. He infiltrated the city's defenses and soon seized control of the Principal Office again, viral activity went "off the spreadsheet" - tens of thousands of Systems were attacked, being either destroyed, infected or fed upon. The Guardian Collective was stretched to its limits, and eventually had to turn to the Codemasters' and their weapon Gnosis. With the triggering of Gnosis, every Virus on the Net was erased. (Paradigms Lost)
- The title for the Viral Wars comes from the name of the fourth Season 3 DVD, and is often used to refer to the entire events of the season.
- Many of the events of the second war were never shown, outside of flashbacks in the episode Megaframe.
- Mainframe was cut off from the rest of the Net for most of the Viral Wars, but it is unclear if this was due to Bob's absence, Mouse protecting Mainframe from the Web, or something else.