One of six predetermined origin stories begins the game, depending on the player character's race and class. Each story ends with the player leaving with Duncan, the commander of Ferelden's Grey Wardens who is seeking new recruits and selects the player as a candidate. The two journey to Ferelden's southern fortress, Ostagar, to join Cailan, the King of Ferelden, and his father-in-law Loghain, a legendary general and close friend of Cailan's late father, King Maric. The three leaders plan to attack the encroaching Darkspawn to stop a new Blight from overwhelming Ferelden. Duncan senses the influence of an Archdemon, a god-like Dragon that commands the Darkspawn, and emphasizes the importance of defeating the Blight before it can threaten the rest of Thedas.
Duncan initiates the player into the Grey Wardens via a ritual called the Joining, which involves imbibing Darkspawn blood. The recipient, if they survive, is granted the Taint, a connection into the Darkspawn hive mind to sense them. After surviving, the player (now nicknamed "The Warden") and fellow Grey Warden Alistair are tasked with lighting a beacon at the top of the fortress to signal Loghain's men into charging the Darkspawn horde flank. However, upon arriving, Loghain abandons the battlefield, leaving Cailan, Duncan, and their army to be slain by the Darkspawn, who seize control of Ostagar and begin advancing into southern Ferelden.
The Warden and Alistair are saved by Flemeth, a powerful witch who lives in seclusion. Flemeth sends her daughter Morrigan to accompany the Warden and Alistair in gathering a new army to combat the Archdemon and stop the Blight. Using ancient Grey Warden treaties, the Warden travels across Ferelden to enlist the aid of the Circle of Magi, the Dalish Elves, the Dwarves of Orzammar, and soldiers in Redcliffe loyal to Arl Eamon. In addition, Alistair reveals that he is a bastard son of King Maric, making him a contender for the now vacant throne. Meanwhile, Loghain returns to Ferelden's capital city, Denerim, to inform his daughter, Queen Anora, of Cailan's death. Loghain scapegoats the Grey Wardens for the defeat at Ostagar and demands the deaths of any survivors. While Anora inherits her husband's authority, Loghain declares himself her regent and seizes control of the kingdom, becoming a tyrannical ruler determined to retain power. Ferelden's nobility rebel against him, igniting a civil war which ends in an inconclusive stalemate and allows the Darkspawn to advance further into Ferelden unopposed.
Eamon then calls a Landsmeet among the nobles of Ferelden to rally the kingdom against the Darkspawn, where the Warden or a party member defeats Loghain in a duel. If Alistair defeats Loghain, he will then execute him. Otherwise, the Warden can either have Loghain executed or recruited into the Grey Wardens and the party in place of Alistair (who quits both in turn). Dependent on this and other past decisions, the Warden then settles who assumes Ferelden's throne (Alistair and/or Anora), with the option of marrying the one of opposite gender if a Human Noble.
Before the final battle, the Warden learns that a Grey Warden must slay the Archdemon to prevent it from releasing a demonic essence which finds a new host in the nearest Darkspawn. The essence will be drawn to the Taint, killing the Warden in the process. Morrigan meets with the Warden and proposes a ritual that will see her conceive a child with a Warden. The Archdemon, upon death, will instead be drawn to the child, born as a demigod with the Taint, sparing the Warden who slays it. Morrigan agrees to conceive the child on the condition that she raise it alone. The Warden can accept Morrigan's offer (if male), convince Alistair/Loghain to take part instead, or refuse the proposal (which causes Morrigan to leave the party).
The next day, the Warden and the newly assembled army gather in Denerim. They repel the Darkspawn horde and vanquish the Archdemon. If Morrigan's ritual was performed, the Warden slays the Archdemon. If not, they must decide whether they or Alistair/Loghain does so and perishes in the process. The remaining Darkspawn retreat from Denerim, marking the end of the Fifth Blight. The story ends with a ceremony attended by Ferelden citizens, where the Warden and their companions are honoured for saving the kingdom. An epilogue details the ramifications of the Warden's choices, including the future of Ferelden, any rumours, and the fates of his or her companions.