The campaign begins when the player is sent to administer a fief granted to him by the Emperor, in the Occident. The Emperor is unwell and Lord Richard Northburgh, cousin and treasurer of the Emperor, is building a magnificent Cathedral to pray for the Emperor's health. Meanwhile, Cardinal Lucius is making preparations for a Crusade against the Saracens of the Orient, aided by Guy Forcas.

In the first few chapters of the campaign, the player learns the basics of game-play and the economy by assisting Northburgh and Forcas with supply and construction tasks, as well as meeting some of the other main characters.

As the Crusader ships leave the harbour, Northburgh begins to uncover clues to a mysterious plot. He and the player travel to the Orient and befriend the Grand Vizier of the Sultan, Al Zahir, who helps the player to defeat a band of Corsairs and break up a child trafficking scheme. The plot thickens as further clues reveal that a main character is implicated in a sinister conspiracy to overthrow the Emperor himself. Because he comes too close to the truth, Lord Northburgh is captured and the player is tasked with unravelling the mystery.

Over the next several chapters, the player must win over new allies, convince the leaders of the Crusade that they are being manipulated under false pretenses, and survive dire circumstances in order to defeat the villains and restore the Emperor to his rightful place.

The campaign is divided into eight chapters and each chapter can be played on 3 different difficulties: easy, medium, and hard. Apart from the story elements, the campaign serves as a tutorial to prepare the player for the more rigorous scenarios and continuous game modes.

All of the main characters encountered in the campaign are also encountered in the scenarios mode and can be selected as computer opponents in continuous games, although the actions of the characters during the campaign are unrelated to their actions in these modes apart from having similar personalities. Lord Northburgh and Al Zahir act as mentors and trade partners in the other modes, much like they do in the campaign.