Dark Soul

A Dark Soul is a NetNavi's soul engulfed by a Dark Chip's influence. Generally, the body of the navi turns black.

MegaMan Battle Network 4
MegaMan uses a dark chip in MegaMan Battle Network 4 as the only way to defeat ShadeMan. Throughout the game, MegaMan is faced with the temptation of using the power of Dark Chips but is able to suppress his dark soul enough to keep in control. Later in the game, it is discovered that Chaud uses a Dark Chip on ProtoMan as a last ditch effort to delete 700 evil navis. ProtoMan's Dark Soul however, has taken over his soul and becomes evil, detaching himself from Chaud. MegaMan chases ProtoMan into the undernet and confronts him. Under the operation of Chaud, MegaMan is able to defeat and capture ProtoMan DS and his dark soul is suppressed.

At the game's climax, MegaMan is forced to confront his Dark Soul in a battle before fighting Duo. MegaMan's dark soul's fighting style is very much developed based on MegaMan's and has the same HP and Navi Customizer parts equipped. MegaMan defeats his Dark Soul and then is able to defeat Duo.

MegaMan Battle Network 5
In MegaMan Battle Network 5, MegaMan gets kidnapped by Nebula forces and receives a "Dark Chip implant" turning into Dark Mega. Nebula places him in charge of controlling End Area 3 and only returns to normal after being defeated by the liberation team.

Anime
In MegaMan NT Warrior, Navis using dark chips will start to develope blotches of black or purple on its body. It should be noted that this only happened to FlashMan and DesertMan. In the animie, MegaMan turns dark after a painful bite to the neck from ShadeMan.