At a space research center known as NAXA, scientists discover a massive asteroid speeding toward the Earth that would cause the extinction of all life.
After a call is put out to the world's greatest scientists, including father of the protagonists Yuichiro Hikari and a man known as Dr. Regal, they decide to direct the asteroid off-course with a laser.
After fighting ShadeMan.EXE, he drops unknown data which is later revealed to be a DarkChip, a program described as unleashing great power at the cost of a Navi's "soul."
Following Regal's suggestion to search for a world class Operator and Navi, Lan and MegaMan are invited to the Red Sun/Blue Moon Tournament in the country of Netopia.
After winning the tourney, the duo travel to NAXA and are briefed on the situation and learn that the asteroid headed for Earth has a computer in it and can be steered away with a Navi.
There are also special chips (like the 5 evil chips) that can only be used if Mega Man is completely consumed by dark power, but the main drawback by using is that Double Soul will no longer be available to use unless the player gets in Full Synchro several times, removing the Dark Soul corruption from Mega Man little by little.
Conversely, if Mega Man does enough battles (about 1000) without ever using a Dark Chip, he will turn brighter in color and allow him to more easily achieve Full Synchro mode.
The Emotion Window is a mood indicator that lets the operator know Mega Man's current state based on fighting performance.
Conversely, when a fight is not playing in Mega Man's favor, unless in a doublesoul, he gains an anxious expression and following this, Darkchips begin to display themselves in the Custom Screen.
The player can return to a normal, calm state by successfully counter-attacking a virus, restoring HP, scoring hits on the enemy, or winning the battle.
If, during battle, Mega Man suffers repeated hits at a rapid rate, or if he is stunned for a period of time, he goes into a state of rage which is similar to Full Synchro in the way that it doubles Battlechip attack power, but instead of a focused expression in the emotion window, Mega Man has an angry expression and in the battle screen he glows orange.
For example, the player may obtain the "Z-Saber" chip by linking their game with a copy of Mega Man Zero 3.
In the previous two games, players earned different colored stars on the title screen for completing certain tasks.
Battle Network 4 replaces these with badges (sometimes called icons or marks instead) on the top of the title screen, and continues these for the remainder of the series.
Battle Network 4 includes seven icons, one for defeating the final boss Duo, one for getting all Soul Unisons, one for collecting all Standard-level battlechips, one for all Mega-level chips, one for all Giga-level chips, one for completing all Program Advances, and the last for defeating Bass (Forte in Japanese) in his Omega form.
If the player leaves, and then returns to, the map while in Park Area during WoodMan's scenario, the game will hang indefinitely.
[1] Capcom of Japan gathered together their surplus of Rock Man EXE 4: Tournament Red Sun and Rock Man EXE 4: Tournament Blue Moon games and put them in a special edition box that was released in Japan only on December 31, 2004 along with a special E-Card for the E-Reader.