
Giga chips are a new addition, giving way to really powerful chips like Balance or Navi Recycle. As you can only hold one copy of a Mega chip in the folder, this prevents the abuse of incredibly powerful chips like Full Custom, which was horribly exploited in the previous game, where it was allowed in 5's like every other chip. Standard chips are now limited to 4 copies per folder, and all Navi chips from the previous game are treated as Mega chips, along with some incredibly powerful chips. This allows for a more balanced folder whilst allowing for amazingly powerful chips to be used.

First, the Library has been split into 4 portions - Standard chips, Mega chips, Giga chips, and Program Advances. Once again, the game introduces a few changs to the folder building system. However, a letter Lan's grand-father left them contained coding that let MegaMan be restored. In its last moments, Alpha absorbed MegaMan, and the navi was thought to have been deleted. In addition to the TetraCodes, Wily, head of When Lan and MegaMan arrived, Alpha was awaken and after a battle with Bass, Alpha appears and devours Wily (who was in the net with a Pulse Transmision Program) and Bass, seeing that they started to fought and destroyed Alpha. The scientists were forced to seal Alpha to prevent further damage. The codes were required for However, he went beserk and devoured any navis and programs. However, the net operators always managed to escape with special programs known as TetraCodes.
Once Lan and MegaMan get into the N1 Grand Prix, the tournament was discovered as a set-up by WWW to intimidate the world about their return. Half of the game involved qualifying for the tournament. A NetNavi tournament called the N1 Grand Prix took place. There are two versions: White (no subtitle in Japan) and Blue ( Black in Japan). MegaMan Battle Network 3 (Rockman.EXE 3) takes place not long after MegaMan Battle Network 2.
