Lan and his family have moved house to Cyber City, which is famous for its new technology. Lan and Mega Man quickly make new friends, and find out about the legend of the Cybeasts, two ancient creatures with such power that they eventually destroyed each other. However, a shady organization is intent on reviving and controlling the Cybeasts for their own nefarious needs, and Mega Man gets caught in the middle! While they capture the phoenix-like Falzar, Mega Man captures the wolf-like Gregar. By harnessing this new power, Lan and Mega Man must save the internet once again!
Mega Man Battle Network 6 is an RPG-like game in which you navigate through both the real world, and the cyberworld of the internet. As Lan, you move through the real world, interacting with people and finding places to 'jack-in' to the cyberworld for Mega Man to take control. As Mega Man, you can fight viruses in a hybrid of turn-based and real-time battle: you select which battle chips you need to use each turn, and then use them while actively dodging enemy fire.
New to Battle Network 6 is the "Cross Change" system. After beating certain enemy Navis, Mega Man can copy their strengths (as well as their weaknesses!) and use them to his advantage, similar to the original Mega Man games. For example, you could take on the firepower of Heat Man, or the cutting power of Slash Man.
At a certain point in the game, Mega Man also gains control of the powerful Cybeast, Gregar. Using this power, Mega Man can transform into a wolf-like Navi, boosting his attack power for three turns, and enhance the power of certain battle chips. If players continue to push Mega Man, he will enter the "Beast Over" state, with even more power, but at the loss of control and a severely weakened Mega Man. It's also possible to combine the Cross Change with Gregar, creating even more powerful attacks.
Like Mega Man Battle Network 5, this game was going to include a "crossover battle" with Boktai 3, as well as references to the Boktai games. However, because of poor sales of the previous Boktai games in the west, Konami decided not to localize Boktai 3. Due to this, nearly all the Boktai references got cut from the localized version of Mega Man Battle Network 6, including some extra areas in the cyber world and various Battle Chips.