Shadow Throne takes place in the Aclysmian empire, where the kingdom and royal family are torn apart in a bitter civil war. King Kyros clings on to power by any means necessary; his estranged Queen Eleftheria has joined a rebellion of conquered people; and their daughter, Princess Beatus, has rejected both of her parents to fight alongside the church.

The players, as members of a secret society, wield great influence over the destiny of Aclysmia, but their job is not to set things right. They just want be on the winning side when the fighting ends. By weaving Machiavellian alliances and determining the outcome of crucial battles, they accrue influence for when the war finally resolves.

Shadow Throne is played over the course of several battles. To start each battle, players gain control over characters from the warring factions by drafting a hand of cards. Next, players simultaneously play cards from their hands to determine which faction wins the battle. Players can freely switch alliances, playing cards from any faction. After the battle is fought, the faction with the most power wins, and players who played cards from that faction collect influence points. Once one player has collected enough influence, the game ends.