Mega Man Battle Network 3

Mega Man Battle Network 3, known as Battle Network Rockman EXE 3 (バトルネットワーク ロックマンエグゼ3) in Japan, takes place not long after Mega Man Battle Network 2. Deviating from the previous installments of the series, the game was released in two separate versions: White (no subtitle in Japan) and Blue (Black in Japan).

Story

Months after the Netmafia Gospel tried to take over the world, Lan Hikari and friends return to their ordinary lives, until the crime organization WWW started surfacing again. At the same time, a NetBattle tournament called the N1 Grand Prix was being held, in an attempt to find the strongest NetBattler in the Electopia, attracting people from neighboring countries into entering. Lan and MegaMan.EXE manage to pass the preliminary rounds, only after numerous attacks by the WWW in an effort to get the TetraCodes. Once Lan and MegaMan get into the N1 Grand Prix, it was discovered that the tournament was a set-up created by WWW to announce their return to world.

Lan and friends, with the help of Eugene Chaud had pieced together the WWW's plan after their attacks on ACDC School and the Yoka Zoo, both of which are hiding places of two of the TetraCodes: needed to revive the monster Alpha, the original prototype of the Internet, and take over the world. As Alpha had went berserk and devoured Navis and programs upon its creation, scientists were forced to seal Alpha to prevent further damage.

Alpha

In addition to the TetraCodes, WWW needed Bass.EXE in order to awaken Alpha. It was revealed that Dr.Wily, head of WWW, was moving behind-the-scenes in Gospel, and had put them to the task of creating a copy Bass specifically for the resurrection. However, this time Wily didn't need a fake Bass because he tricked the true Bass into removing the final security measure on Alpha. When Lan and MegaMan arrived, Alpha was awakened and after a battle with Bass, Alpha appears and devours Wily (who was in the Net via a Pulse Transmission) and Bass. Seeing that, the duo fight Alpha. Once they destroyed Alpha, a door appeared, leading to a Vision Burst of SciLab, where Lan (also on the Net) and MegaMan meet Tadashi Hikari, Lan and Hub's grandfather. Being only personality data, he was only able to give Lan and MegaMan an encoded letter to be delivered to Lan’s father, and also remarking on how well Lan and Hub had become great friends and brothers, before the Vision Burst within Alpha collapses. Before being able to jack-out, Alpha captures Lan and MegaMan and begins devouring them, until MegaMan sacrifices himself to save Lan. MegaMan was thought to be deleted, until Lan's father finally decoded the letter from his father, which contained MegaMan's backup data, and Tadashi Hikari's personality data.

Changes from previous games

Chip Folder

Once again, the game introduces a few changes to the folder building system. First, the Library has been split into four portions – Standard Chips, Mega Chips, Giga Chips, and Program Advances. This allows for a more balanced folder whilst allowing for amazingly powerful chips to be used.

• Standard Chips are now limited to four copies per folder, and all Navi chips from the previous game are treated as Mega Chips, along with some incredibly powerful chips.

• As players 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 five's like every other chip.

• Giga Chips are a new addition, giving way to really powerful chips like Balance or Navi Recycle, and only one Giga Chip is allowed in each folder.

Navi Customizer

NaviCust Screen

The Navi Customizer (NaviCust for short) is introduced in this game. Instead of receiving PowerUps which are used to permanently upgrade the Buster, MegaMan now receives NaviCust pieces that grant him different abilities like the ever-useful Undershirt. Some parts of the plot also require the use of certain parts, like Press and Black Mind. This game is the only one in the series that uses Extra Codes and Color compatibilities, seeing that after MegaMan loses Styles in the following game, the codes and compatibilities are of no use afterwards and are hence scrapped.

Style Change

Heat Shadow Style

Style Change now serve a different function. Leveling up MegaMan's style no longer improves the damage of his charged Buster, but instead grants him special NaviCust pieces that can be used with the Style. Some existing Styles are also given new innate abilities, like the Custom Style's ability to yield special chips when S-ranking viruses. Three new Styles are also introduced, with two of them being exclusive to either version (Ground, Shadow, Hub). However, MegaMan can now only hold one Style.

Bug Frags

Finishing off opponents while they are in the midst of attacking - also known as Countering - will now give Bug Frags. These are used in many areas - for trading, virus breeding, and for trading at the Bug Frag Trader. This game also introduces the Number Lottery, where the player can input a certain number code to get an item. Often these items would range from subchips to rare chips unobtainable through any other means. 

Version differences

Serenade

Both versions have identical plots, but distinct qualities unique to each game. White has the standard appearance of buildings and objects, evidenced by ACDC Town's squirrel statue, which is always pink. However, Blue has new color schemes for buildings, and some objects are totally different, such as the squirrel being gold (a color change that becomes prevalent between both game variations in later installments).

This is also the first time different chips can be obtained in separate games, such as unique, one-of a kind Giga Chips, which also becomes the standard among the later games. Giga Chips cannot be traded, but in this game, the Omega Navi Giga chips are actually duplicated.

The games also have two separate bosses working with Serenade. White has MistMan.EXE, but Blue has BowlMan.EXE. As such, their chips must be obtained through NetBattles, not a Chip Trader, and even then, the Mega Chip library isn't complete until the chips of both Navis are traded between separate versions.

Secrets

There are secret achievements that can be activated in both games. One Giga Chip is only obtained by NetBattling a friend while both players have at least three stars, and then S-Ranking the friend. It has a 1 in 32 chance of showing up, but can only be obtained once, and these odds improve with additional stars, like the ten secret chips in Battle Network 2.

Even more secrets can be activated at five stars. By holding Left on the D-pad on the GBA at the Start screen and inputting the code, R R L R L R L L, the stars move closer together and make room for two more. After this, fifteen Omega Navis will surface on the Net to fight, and beating them grants the player another star. Finally, using a Program Advamce only usable with KingMan V5, BowlMan V5, or MistMan V5, will finish the library of 32 Advances, the largest P.A. library to date.

Lastly, this is the first time that a final boss will grow stronger after completing all the sidequests. Alpha evolves into an Omega form with new attacks, sporting more HP, after all seven stars are obtained. By beating him, his Giga Chip can be obtained to completely finish the game.