The plot of Beyond the Dark Portal takes place after the events of Warcraft II: Tides of Darkness. The Orcs, now under the leadership of the shaman Ner'zhul, staged a new invasion of Azeroth and overwhelmed the citadel of Nethergarde, which guarded the remnants of the portal. The Alliance itself had been splintered after the Second War and Gilneas and Stromgarde had withdrawn their support. The arch-mage Khadgar summoned heroes of Azeroth, Alleria Windrunner, Danath Trollbane, Turalyon and Kurdran Wildhammer to rally the forces of the Alliance. The Horde was beaten back and Khadgar decided to take the initiative to push through the Portal into the Orcs' homeland. Before being pushed back, Ner'zhul managed to steal the spellbook of Medivh which was needed to create new Portals.
The Alliance gained a foothold and made preparations to seal the rift forever while the Orcs reorganized. Khadgar needed the spellbook of Medivh and the Skull of Gul'dan to accomplish it. They razed the Shadowmoon Citadel, seat of Ner'zhul's Shadow Council. While the Alliance army and navy only barely held out, Khadgar managed to acquire the items with help from the Laughing Skull Clan. Ner'zhul managed to open portals to the Twisting Nether and escaped through one of the new Portals. The violent energies began to destroy Draenor and also threatened Azeroth. Khadgar destroyed the Portal on the side of Draenor to prevent harm to Azeroth, trapping the remaining Alliance forces beyond the Dark Portal in the dying land of Draenor. Khadgar and the warriors of Azeroth then entered one of the portals not knowing where it would lead to avoid being killed by the violent rifts tearing the planet apart.
After the Second War, the Alliance loses the allegiance of the elves, who accuse the Alliance of not having done enough to defend their home, and of two Human kingdoms, which advocated exterminating the remaining Orcs rather than keeping them in captivity. One Orc clan that had fought in the Second War's final battle was unaccounted for. Although the Dark Portal had been destroyed, a tear in reality hovered over the ruin.