The FactoryComp is a sinister and creepy network with several DarkChips on the background and black puddles on the main road.
To progress the player needs the cooperation of the respective Team's Navis as the path is blocked by barriers which can only be opened with specific switches. The switches, however, are blocked by obstacles that only the proper teammate Navi can surpass. As such the bulk of the network is using the other Navis to create a path for MegaMan.EXE for him to further allow access to his teammates and progress deeper.
At certain intervals, a dark substance will fall over whichever Navi is being controlled. If the substance touches the Navi, they will take damage.
Team ProtoMan/Colonel enter the network when assaulting Nebula's base. The multiple operators are forced to cooperate as they make their way through several security blocks that close access to further levels of the Dark Chip Factory.
As they progress several of the Navis are lost as a result of the Darkloids summoning the Dark Galaxy in order to absorb them and eliminate threats. Only MegaMan is spared from this fate who along with Lan, make their way towards Dr. Regal's SoulServer.