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Like its name suggests, the area is a large graveyard, with the tombs of all the NetNavis in the game. The first area, exclusive only to the Japanese Version, holds the graves of all Navis from the first game to the fifth game. To access Graveyard 2 from Graveyard 1, the player needs to complete his Mega Chip Library first. Gregar or Falzar Beast MegaMan can be randomly encountered in this area after Forte BX's defeat.
Graveyard 2, the only Graveyard area in the US version, holds the graves of all Navis in BN6. A door can be opened with the BatKey to get an AttackMAX NaviCust program. There is a gate halfway through that requires the player to complete his Standard Library first. After getting past it, there is a few more graves and a huge staircase. Up the huge staircase is a huge platform with a gravestone. MegaMan notes that the gravestone is blank, and Bass.EXE appears, telling him that the gravestone was meant for MegaMan himself. Bass then proceeds to engage him in combat, only to be defeated again.
In the Japanese version, Graveyard 2 does not hold the AttackMAX part or the BatKey's gate, and it also possesses another exit into Graveyard 1. This exit leads to the grave for the Navis of Rockman.EXE 4.5 Real Operation.
Afterwards, all the tombstones belonging to the antagonistic Navis have an eerie glow to them and when MegaMan examines them, the NetNavi whose tomb it belongs appears in its RV form to battle. The reward for the battle will always be 3000 Zennies. The graves will start glowing again if MegaMan jack out, jack in again, and go back to the Graveyard Area. After Bass BX's defeat, he also can be randomly encountered in this area.