In The Games
 Mega Man Battle Network
PharaohMan appears as a secret boss after MegaMan and Lan defeat the Life Virus. Once MegaMan reaches level 70, he will appear at a dead end in Internet Area 12. After defeating him once, he reappears as a random encounter in the same area.
 Mega Man Network Transmission
PharoahMan appears in the legendary WWW Area, an area with similarities to Pharoah Man's original series stage complete with a remix of that stage's soundtrack. He has 1000 HP, and defeating it is necessary to retrieve the OldData.
 Mega Man Battle Network 2
PharoahMan makes a third appearance in Mega Man Battle Network 2. This time he appears in an area that can't be accessed until after defeating the Gospel Beast. It appears in an attempt to stop MegaMan from advancing in WWW Area 1, and while the battle is similar to the battle in Mega Man Battle Network, it falls all the same.
 In The Anime
PharoahMan plays a critical point in the plot of Mega Man: NT Warrior, as he was awakened as a result of the N1 Grand Prix Finals between MegaMan and ProtoMan. The solo NetNavi would attempt to delete ProtoMan, but MegaMan jumps in the way, taking the fatal shot and getting deleted. PharoahMan would proceed to use his powers to sink that artificial island into the ocean, then causing widespread problems throughout the Net.
It was revealed that PharoahMan was once created to monitor and guide data flow across the Net, deemed so powerful to be an ultimate NetNavi by Lord Wily. Dr. Hikari found that a virus had infected his systems and thus took him off line.
WoodMan, SharkMan and SkullMan would attempt to stop PharoahMan's rampage, but they would be turned to stone but they did cut his power before being rendered inanimate. ProtoMan would try to stop him as well, but didn't have much luck until the recently revived MegaMan joined him. It took a Double Program Advance to stop PharoahMan, burying him within the ruins of the base he himself had built. StoneMan and BlasterMan would capture the wounded NetNavi and attempt to reprogram him, but PharoahMan would self-destruct, severely damaging WWW's base in the process.