This section includes not only the backstory of the games, but also the plotline as it stands at the end of this game. Don't read this before completing it, unless you have no gaming soul. You've been warned.

The creation of Alpha, and the banishment of Bass

Twenty years before the first game begins, Light Hikari, grandfather of Lan and Hub, was the top scientist in all of Japan. After inventing networks and devices called PETs, he embarked on his largest project to date, a prototype internet society that would link every network together, the basis of a future net society. This prototype, called Alpha, had to be thoroughly tested and refined before it would be ready for the world to use. And so for 10 years, it was studied and worked. Then, one day, all of the networks connected to Alpha for testing were suddenly went down. After careful study, the scientists on the project concluded that it was not Alpha which was buggy, but another project that the science labs were working on, the self-programming Navi project led by a scientist called Cossack. The project had designed the world's first automatic navi, one that could carry all its own chips, access networks without human help, and had a Get Ability program Cossack had designed that allowed the Navi to copy any chip or program and use it himself. That Navi was called Bass. However, because the timing of the testing of Bass happened the same time Alpha went nuts, the scientists blamed Bass.
    The project was deemed a failure and Bass found to be too dangerous, so the scientists sent the strongest Navis designed by the Officials, the Navi Elite Unit, to delete him. Bass was able to save himself and escape, but he was scarred from the battle and started wearing his cloak. Ever since that day he had been wandering the net, fighting off viruses in daily battles for survival. Over time he collected the strongest powers he could find, challenging the most powerful Navis on the net, knowing that he would one day gain the ultimate power, and then sit in judgement of those who had betrayed him and cast him into the net alone.

The sealing of Alpha, and hiding of the Freeze

Meanwhile, believing Bass to be destroyed, the scientists expected that the problem with Alpha would be solved. They were wrong. For years, a virus had been growing and multiplying inside Alpha undetected, increasing in power and even developing it's own AI. It begam absorbing and feeding off programs and Navis, growing larger and stronger. One day it suddenly devoured all the networks connected to it. The scientists tried to find a way to destroy the virus inside Alpha, but it was too powerful to handle and all attempts only made the situation worse. Another scientist developed a powerful hindrance program, Freeze, that could potentially freeze Alpha, but this cure turned out to be potentially worse than the disease, since only the most powerful Navis could handle it, and if used wrongly it could freeze the entire net forever. With his dream of networks becoming like a nightmare, Light developed the"Guardian, a barrier which would contain Alpha until a solution could be found. Feeling responsible, he transferred a copy of his mind into the Guardian, to watch over Alpha and ensure his own creation would never escape. Finally, after about a week of devouring everything in sight, Alpha's activity began to slow. Light used the time start planning. It was a success, and Alpha was contained. After the incident, which was later called the Alpha Rebellion, Alpha and Light's copy were sealed away into the highest level top secret in the science network, protected by the Tetra Code. Sealed away, they hoped, forever.
    Cossack, saddened by the failure of Bass, left the science labs and started an independent Navi company, which would later become one of the most successful in the world. The dangerous Freeze was sealed far away from the mainstream society into the enormous, shady network area known as the Undernet. Its obscurity would later make it a popular hangout for the criminal population of the net, for whom the original purpose of the area was unknown. The Freeze would be protected by the Undernet Ranked Navis, some of the strongest in the net. If ever a day came when the program would be used, only a Navi who could climb the Ranks would be strong enough to use the program.

The creation of Gospel, and Bass's role

Ten years later, to NetMafia Gospel. After his Dream Virus failed to destroy his old rival's network society, Dr. Wily has went into hiding to rebuild his ranks. One day in the net he came across a lonely boy who had lost his parents. The boy had become quite wealthy from his parent's death, but was angry at the world and lost in remorse. Wily saw an opportunity, and began manipulating the boy into doing his dirty work for him. He convinced the boy that the world was corrupt, and that he should take control of the net, wipe out the old ways and create a new order. At first Wily's plan was to use the boy to create chaos, but then Wily discovered information on Alpha, and developed a new plan to use it to destroy the Net for him. But to break the Guardian program, it would require the assistance of an enormously powerful Navi. No such navi would willingly help him, so he tried to enlist the Legendary Navi himself.
    Bass, who could copy any power, was the only Navi capable of such a feat. Wily attempted to make his own version of Bass by fusing bred viruses with special programs he had the boy gather for him. However, this ended in failure, and instead of a pure copy, a multibug organism with great but uncontrollable power was born. The attempt caught the attention of Bass who took it upon himself to destroy the remaining copies of himself running around. Wily struck a deal with Bass to help him destroy the Guardian, convincing him that absorbing the Guardian's power would make him the strongest in the world and enable him to get the revenge he sook. Although Bass hated Wily as much as any other human, the thought of such power was tempting, and the two formed a wary alliance.

The destruction of Alpha, and the fusion of BassGS

Fast-forward to the end of this game. Alpha is stolen by Wily, and Alpha-Bugs have begun leaking out all over the net, creating paths to hidden systems, even into military computers. However, the core of Alpha is still sealed. As Lan and his friends invade the WWW base, Wily and Bass prepare to destroy the final Guardian and set Alpha free. Wily uses the Pulse Transmission System to plug himself into the net, and Lan and MegaMan go in after him. As they arrive, Bass shatters the Guardian with his powerful Earth Breaker, and absorbs its power. MegaMan and Bass do battle, which MegaMan wins. Bass is amazed, but Wily is indifferent, remarking that he was hoping the two would destroy each other. He reveals that now that the Guardian was destroyed, Alpha would flood the net, destroying the network society and plunging the world into anarchy. He laughs as Alpha absorbs the battle-weakened Bass, but his joy is short lived when Alpha absorbs Wily as well. MegaMan and Lan use all their power to destroy Alpha, and to their surprise, find a doorway where Alpha once rested. Inside, they meet the ghost of their grandfather, Light Hikari, who had met them only when they were babies. After a heartfelt reunion, Light gives them a letter to give to their dad before Alpha begins to collapse. Confident that the future of the world is in good hands, Light is finally ready to delete this last copy of his consciousness, and stays in the collapsing Alpha while Lan and MegaMan make their way out. While pausing for only a moment, the two are swallowed by Alpha, and MegaMan decides to use the last of his power to blow Lan free and back to his body in the real world. He bids his brother goodbye, and Lan is expelled from the network. The others find him, and the group returns for a reunion with family and friends. Meanwhile, Bass barely managed to escape death once more, but this time he's extremely weak. To his surprise, he is found by Gospel, the wolf-like partial clone of himself, who had regenerated from bugs which were spread across the net after it's initial destruction. Bass realizes that the creature wants to help him, and the two are joined and begin to regenerate using virus power, forming the more powerful BassGS.