The time period of Vindictus is set several hundred years before the era of Mabinogi: Fantasy Life. In this war-torn world, the Humans cling to the belief that if they can destroy the Fomors —monstrous humanoids— they will be brought by their black-winged goddess, Morrighan, into the land of Erinn and be enriched in paradise. As a result, the land has suffered under endless war for hundreds of years, and many people are beginning to give up hope that the legend of Erinn is real.

The gameplay all begins at Colhen where several soldiers of the Crimson Blade Mercenaries are attacking a Giant White Spider scaling a bell tower. Tieve, the Oracle to the Goddess, steps in front of the ballistae to prevent them from firing. Captain Aodhan demands her to step aside as the Spider has become a monster rather than the town's guardian. Tieve refuses, begging them to allow her to communicate with the Spider. Aodhan eventually agrees as Tieve wouldn't obey, and brings a few of his men into the tower. However, he finds a Fomorian Emblem in the tower. He questions the appearance of the Emblem, but he and his troopers are ambushed by Gnolls within the tower, leaving only the Player to defend Tieve.

When the two reach the top, the Spider begins to calm down at the sight of Tieve, but becomes enraged again. It is then challenged to a death battle by the Player who is supported by ballistaes. After a long, gruesome battle, the Spider attempts to further climb the tower, only to be shot down by the ballistaes and finished off when several large fragments of the building fall on it. Tieve mourns the death of the Spider, but there is no hope left for it. While Tieve cries, the camera zooms back to a mysterious character who has been watching the events this whole time, and leaves at the sight of the killed Spider.

To begin the real journey, the rookie goes through training, and is introduced to Colhen, its NPC characters, vindictus gold and simple gameplay. Then they move onto more serious issues in Perilous Ruins, as they are to investigate why the Gnolls attacked Colhen in the prologue.

Through a series of battles, the Crimson Blade Mercenaries learn that the Gnolls are indeed working for the Fomors and you are dispatched to try to destroy its forces. They fight through powerful resistance until they reach their first real challenge: the Gnoll Chieftain, the leader of the Gnolls in the Perilous Ruins. After his defeat, the situation within the Perilous Ruins is over, but the war against the Gnolls may not have been won.