The Sneaking Suit and the Skull Suit protectors are both references to the Metal Gear series.

There is a mission in which you must purify a coffin that contains "Shademan." During the fight, Django will work with Mega Man to defeat Shademan.

Shademan's final words are:
"Once more... I...! ...Don't think... ...that I will disappear... ... in THIS world...! And again... back... ...to the... ...the Cyberworld...!

Unfortunately, due to poor sales, the side mission in Mega Man Battle Network 6 that goes along with this side story was removed completely, but was available in the Japanese version "Rockman.EXE 6."