- Japan: December 14, 2001
- North America: June 17, 2002
- Europe: October 18, 2002
The following summer after WWW's defeat, a new terrorist group called Gospel emerged. Their tactics differed considerably compared to WWW, as they appeared to have no set goal. Gospel's plan had seemingly consisted of only causing random destruction with their NetNavis. Lan and MegaMan battled every member and prevented the worst possible situations. However, Gospel's hidden plan was to re-create the ultimate NetNavi, Bass.EXE (Forte.EXE in Japan). Using bug fragments, they planned to make a large army of Bass navis to take over the world. Unknown to Gospel, their method of creating Bass was imperfect, and his abilities were vastly below predictions. In an attempt to increase Bass's power, the leader of Gospel overloaded energy into Bass, and changed him into a giant multi-bug organism, who was called Gospel as same as the organization. Although the bug beast was stronger than before, Lan and MegaMan managed to elminate it.
- At one point in the game, an old lady will complain that her oven is on fire, and wonder what Lan meant by "that's an old story". said event happend in the first game.