Unlike all the other Mega Man Battle Network games, there is no set order to the story, as the individual scenarios occur randomly.
At least everyone fights this boss first, regardless of version.
Well, this has to be the strangest boss I've ever fought in the Battle Network series. When you first fight him, you can't damage him, but if you hit him 10 times with any attack, the battle will end. When you meet him the second time, you cannot hit him with normal chips... only a Darkchip that you get during the battle. To fight him proper, you'll have to wait until you reach the Undernet, and has a link to the Botkai side quest involving Django and Otenko from the Botkai series. Watch out for his bat summoning ability, which isn't very dangerous, but is quite annoying. What you should watch out for is Big Noise, which can cause quite a bit of damage, and can either stun you, or confuse you, leaving you exposed for suffering a LOT of damage. All in all, when you do defeat him in the Undernet, you can get his chip Shademan S, which replicates his Big Noise attack, and can, when combined with other chips, form the "Big Noise" Program Advance, which releases the supersonic waves further, and does a lot more damage.