The gameplay in Battle Network 3 is similar to that of its predecessors, with no graphical enhancements and minor gameplay changes. Gone are the Power-Ups that were to be collected to improve the MegaBuster - instead the Navi Customizer is added, allowing abilities to be added on with certain rules as to how these abilities can be added with respect to each other.
In Battle Network 3 the virus breeder is available, where special, friendly viruses (that must be found first somewhere in the net) are kept and can be fed using BugFrags. When a virus is found and put in the breeder, a chip for that virus is obtained. Feeding each virus BugFrags levels up their chip accordingly. After a family of a certain type of virus has been fed to the max, they will release information to the player as to where the Omega Virus of that family (i.e. For the KillerEye family, they will give you a clue to find KillerEye Omega) can be found. After the Omega Virus of that family is found and deleted, it will join the others in the Virus Breeder and will be available when the corresponding Virus Chip is used. This is the only Battle Network game that features non-Navi Omega viruses.
Battle Network 3 introduces further classification of Battle Chips by splitting them into three categories: 200 white Standard chips, 85 blue Mega chips and 25 pink Giga chips. Standard Chips are limited to only four of each kind (even if letter codes are different) per folder. Mega Chips are limited to only five per folder, and only one of each kind. Only one Giga Chip is allowed per folder and only one copy of each Giga chip exists throughout the entire game. These specifications would continue for the remainder of the series. There are certain types of programs (see Navi Customizer) that can boost the Mega and Giga chip limits, though. There are five unique Giga chips exclusive to each version and this would continue for the remainder of the series, although Battle Network 5 offers six Giga chips per version. There are also Program advances which are a combination of three or four chips.
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