The First War brought the Fall of Azeroth, following the Orc campaign in Warcraft: Orcs & Humans. The survivors of Azeroth have fled by sea to the Human kingdom of Lordaeron, and the Orcs have decided to conquer Lordaeron, in what is known as the Second War. Both sides have acquired allies and new capabilities, including naval and air units, and more powerful spellcasters.

In the Second War, the Orcs are successful at first, but the Humans and their allies take the initiative, partly thanks to an Orc rebellion initiated by the warlock Gul'dan, who seeks to raise the sunken Tomb of Sargeras. Eventually, the Alliance forces push the Horde to Blackrock Spire, but Anduin Lothar, commander of the Alliance, is slain there. At the final battle around the Dark Portal in Azeroth, the Alliance exterminates one Orc clan and captures the Orc supreme commander and the remnants of his forces. Hoping to avoid further invasions, the Alliance destroys the Dark Portal.