Fortress Shadowmoon was the seat of power of the Shaman Ner'zhul and the Shadowmoon Clan, located on Shadowmoon Valley. It was also the last bastion for his Order of the Death Knights. Its towering spires reached upwards as obsidian blades to cleave the hostile amber skies above. The Alliance pressed its attack and destroyed the fortress in hopes that with destruction of the dark fortress and claiming the Book of Medivh, Khadgar would be able to close the rift between Azeroth and Draenor, to be rid of the orcish hordes forever. They also hoped to eliminate Ner'zhul and his death knights. Although the Fortress of Ner'zhul had been destroyed, and the Alliance managed to scatter the the Death Knights, neither the shaman nor the Book of Medivh were found. Khadgar and Turalyon used their magic to search the ruins for some clue as to the location of the mystic tome, but could not find any. Members of the Laughing Skull Clan had seized the book from Ner'zhul's stronghold before the Alliance armies could destroy it. They later planned to use it as a bargaining tool in order to convince the Alliance to help them destroy a stronghold of the Thunderlord clan in Blade's Edge Mountains.
Shadowmoon Ruins (WC3)
Perhaps the reference to Shadowmoon Ruins in the map of Outland map in The Frozen Throne was intended to be the ruins of Fortress Shadowmoon, although it was located in wrong position by being shown to be part of southern Hellfire Peninsula. Alternatively Shadowmoon Ruins could be intended to just random ruins of previously unknown Shadowmoon landholdings in Hellfire Peninsula. ...or they may be ruins of what was once part of the southern Peninsula, now known as Shadowmoon Valley.
What the designers had intended is entirely unclear.
Black Temple (WoW)
Both the Black Temple dungeon trailer and the novel Rise of the Horde claim that the Temple of Karabor, the sanctum of the draenei leader Velen, was captured by orcs for a time before it became the sinister fortress of Magtheridon, and was in fact used as the headquarters of the Shadow Council until they departed for Azeroth. Afterwards, the temple appears to have been used as the home base for the Shadowmoon Clan under Ner'zhul.
This suggests that the Shadowmoon Fortress assaulted in WarCraft II was in fact another name for this structure. Although this would imply that Alliance didn´t manage to destroy Fortress Shadowmoon and Warcraft II's story was ignored or retconned.