Pentiment

In 1518, Andreas Maler is serving an apprenticeship as an illuminator at Kiersau Abbey near Tassing. Baron Lorenz Rothvogel, a friend of the Prince-Bishop of Freising and longtime benefactor of Kiersau, pays a visit to check on a manuscript he commissioned. Unhappy with the work of the illuminator, the elderly Brother Piero, he insists that Andreas complete the remaining illustrations. The baron is found stabbed to death the following day. Fearing that the murder could damage Kiersau's reputation and lead to its dissolution, Abbot Gernot blames Piero for the crime and has him detained until the archdeacon can conduct an inquiry. Andreas believes Piero is innocent, however, and begins an investigation of his own. He soon discovers several townspeople had reasons to murder the baron, and each received a mysterious note trying to manipulate them into attacking him. Andreas presents his evidence to the archdeacon, and one of the suspects is executed.
In 1525, Andreas returns to Tassing to find the town on the verge of revolting against the abbot's heavy taxation, having been inspired by the Twelve Articles. The leader of the rebellion, Otto Zimmermann, is found dead, and the townspeople accuse the abbot of the murder and threaten to storm the abbey. Andreas once again investigates the crime and finds several townspeople received the same kind of mysterious notes he found seven years earlier, all trying to manipulate them into killing Otto. He makes an accusation against one of the suspects, who flees to the mill and is killed when the townspeople burn it down. The townspeople then set fire to the abbey and its library; Andreas runs into the flames to save the books and is presumed dead. The Duke of Bavaria's soldiers arrive to restore order, killing many of the townspeople in the aftermath.
In 1543, the player assumes control of Magdalene Druckeryn, a young printer and artist. The town council hires her father, Claus Drucker, to paint a mural depicting Tassing's history, but Claus is wounded by an unknown attacker and left bedridden. Magdalene takes up his job and begins piecing together the town's controversial past. She also discovers that Andreas survived the fire and lived as a hermit in the ruins of the abbey for twenty years. The two discover a Roman temple below the town's church and find out that the town's priest, Thomas Sprecher, was the mastermind behind the events. Thomas, not wanting the townspeople to discover that the town's patron saints were actually reinterpretations of Mars and Diana, orchestrated the murders as well as the attack on Claus. He then collapses the temple to prevent its discovery, killing himself in the process. Andreas and Magdalene escape, and the latter decides to finish the mural. Claus eventually dies of his injury, and Magdalene decides to leave Tassing for Prague, while Andreas remains in the town to start a new life.