The gameplay of Mega Man Battle Network 6 is largely identical to that of its predecessors. The player explores the real world through Lan and the Net through MegaMan.EXE. When Lan plugs his PET, a handheld computer, into a computer with an interface jack, he can upload MegaMan.EXE to the cyber network, allowing him to explore and fight viruses as random encounters.[5][9]
When MegaMan encounters viruses, the screen shifts to a battle screen set on a six by three square grid. On the left half of the grid is MegaMan, and on the other half are his opponents. MegaMan has a relatively weak arm cannon, the Mega Buster, but his main weapon is Lan's library of battle chips, one-use-per-battle special attacks which grant various abilities, including simple attacks, attack enhancements, defensive effects, terrain transmogrification, or assistance from other NetNavis. Before battle, the player can construct a folder consisted of thirty battle chips, and each turn of a battle (measured by a timer bar at the top of the screen), the player is presented with a random selection of these chips. The player can send MegaMan up to five Battle Chips, after which the battle takes place in real time, with MegaMan, controlled by the player, attacking with his Mega Buster, dodging attacks, or activating battle chips from his queue.[5][9]
Succeeding the Soul Unison (Double Soul) system, is the Cross System. Although similar to the preceding system in Battle Network 4 and 5, Crosses can last for the entire duration of a battle without utilizing the three-turn limit and can be activated without a sacrificial chip. Upon finishing an ally Navi's mission and battle, MegaMan will gain the Navi Link to that particular Navi, thus enabling a Cross between MegaMan and the corresponding Navi; said transformation can be activated at any time and lasts indefinitely, but are disabled for the rest of the battle if hit my its elemental weakness;[5] gained Link Navis can also be freely used to move around the internet, and function similarly to MegaMan's allies in Battle Network 5, but have a fixed jack-in point. The Link Navis and Crosses gained differ depending on the version played.[9][10][11] Beast Out is an additional gameplay element after MegaMan encounters one of two Cybeasts. This feature can be activated by pressing the "Beast Button" in the Custom Screen, and also differ depending on the version played; Beast Out only last three turns, and can be combined with Soul Crosses.[9] Attempting to Beast Out when the counter is already zero will cause MegaMan to "Beast Over", which results in him moving and attacking uncontrollably for a turn, after which his HP will deplete and be unable to use Crosses or Full-Synchro.[5][9]
There are many other small changes, including chips now being limited by their MB size, alongside their type; players can also "tag" 2 Chips in their folder as long as the combined size is below 60 MB, which will cause them to randomly appear together in the Custom Screen. Another one is a slight change in the Navi Customizer, in which parts can be placed off the map, allowing the player to install more programs, but at the risk of having a bug.[10] Like previous entries, players are able to fight and trade with each other using the Game Boy Advance link cable,[9][11] now including support for the Wireless Adapter.
