Story
Three months following the events of Mega Man Battle Network (two following Network Transmission; both game facts), the story opens with the world in a time of peace following the defeat of the organization known as the WWW. However, NetCrime, as perpetrated by a NetMafia organization known as Gospel, is on the rise. Once again Lan Hikari (known as Netto Hikari in the Japanese version) and his NetNavi MegaMan become involved and work to defeat Gospel’s plot to destroy society.
NetNavis Operators are given the chance to become City NetBattlers, a lesser form of an Official NetBattler, which Lan does, allowing him to travel around the world, both in cyberspace and in real life. In doing so, Lan befuddles Gospel’s attempts to collect four particularly powerful computer programs, called simply SuperPrograms, on numerous occasions. However, Gospel is finally successful and uses these programs, in combination with computer bugs, to construct a SuperNavi of immense power. This Navi is a duplication of Bass, who appeared in the original game as a hidden boss and who plays a larger role in later games. However, after fighting Megaman the Bass copy destabilized and transformed into a gigantic, wolf-shaped super Multi-bug Organism (Also referred as Gospel) that heavily resembles the sixth game's Gregar. The energy needed to create this Navi causes unusual radiation, blending the Net and the real world together. This radiation eventually paralyzes Lan, effectively making him incapable of operating MegaMan, however the latter puts the two into full synchronization so that Lan may control MegaMan by thought and emotion, similar in concept to the final confrontation of the original game.
During the final battle it is revealed that the leader of Gospel is Sean Obihiro, a child who felt neglected by and resentful of society after his parents died in a plane crash. After defeating the Multi-bug Organism Gospel, Lan promises to be the boy’s friend after he has paid for his crimes. After the credits, Bass is seen destroying copies of himself, and shows anger toward the human that made them (implying to Sean). He swears he'll exact his revenge on the humans and then disappears.
Read more about this topic: Mega Man Battle Network 2
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—William Gass (b. 1924)
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“The child ... stands upon a place apart, a little spectator of the world, before whom men and women come and go, events fall out, years open their slow story and are noted or let go as his mood chances to serve them. The play touches him not. He but looks on, thinks his own thought, and turns away, not even expecting his cue to enter the plot and speak. He waits,—he knows not for what.”
—Woodrow Wilson (1856–1924)