Lan and Mega Man return in the fifth entry to the Battle Network series of games. In this sequel, a mysterious group is distributing Dark Navi chips in the hope of corrupting Navis worldwide. Lan and his friends must storm the Dark Chip Factory and put a stop to this problem before it becomes any worse.
The game uses an RPG style over-world in which Lan and Mega Man navigate and interact. In the real world, you control Lan, and can interact with objects and talk to people. When you need to enter cyberspace, you 'jack-in', and take control of Mega Man. Mega Man must also battle viruses in addition to navigating through the internet. This is done with a combination of action and turn-based battle, where you select powerful chips to give you an edge each turn, then use the chips and dodge shots in realtime.
The game also features Liberation Missions, which are a more traditional turn-based style of play. In this mode, you must 'liberate' dark tiles on your way to confront the boss. Liberation Missions play somewhat like a complicated game of chess, with the player actually fighting the battles between the pieces.
Unique to this version of the game is the ability to play as Protoman partway through the story. The game can also link up to Mega Man Battle Network 5: Team Colonel to trade and complete your battle chip collection - certain chips are only available in one version of the game.