An opening prologue details the history of the continent of Thedas; according to the scriptures of Thedas's central religion, the Chantry, a thousand years ago sorcerer-lords from the ancient Tevinter Imperium tried to conquer the Golden City, the heavenly seat of the Maker, and claim the power of God for themselves. Instead, their corruption and hubris irrevocably poisoned Heaven, and for their crime, they were cast back to earth, twisted and mutated into the first of a race of monsters called the darkspawn. The darkspawn multiplied into a horde that swarmed across the world, destroying everything in their path and threatening every race in Thedas with extermination, until an order of warriors called the Grey Wardens arose to combat the darkspawn. Four times the darkspawn have tried to destroy the world in immense invasions called 'Blights' and each time the Grey Wardens have defeated them.
The opening of the story, which takes place in the kingdom of Ferelden, to the south of Thedas, involves a unique origin story dependent on the player character's choice of race, ability and gender. The choices are to be: a son or daughter of the noble family of House Cousland (Human Noble), a member of the elven Tabris family (City Elf), a hunter from one of the nomadic Dalish elf clans(Dalish Elf), a son or daughter of the dwarven royal family, House Aeducan (Dwarf Noble), a castleless vagrant of the dwarven peasant classes (Dwarf Commoner) or an elven or human member of the Circle of Magi (Mage). A series of events end with the player character coming to the attention of Duncan, the commander of Ferelden's Grey Wardens, who is looking for new recruits to combat the start of what is believed to be potentially the Fifth Blight in southern Ferelden, who offers the player character a place in the Grey Wardens.
The new Warden travels with Duncan to Ostagar, a fortress in southern Ferelden on the borders of a forest the darkspawn are said to massing an army within. There, they are introduced to several important characters in Fereldan society, including King Cailan Theirin, the young and idealistic King of Ferelden, and Loghain Mac Tir, Cailan's father-in-law, his most trusted general and a veteran war hero beloved by Ferelden's people. The new Warden encounters Alistair, a junior member of the Grey Wardens who provides background on both the Wardens and their current situation; Ferelden's army is mustering to confront the darkspawn at Ostagar because Duncan is insisting he can sense the presence of an archdemon (supposedly one of Tevinter's Old Gods incarnated in the form of a powerful and corrupted dragon with complete control over the darkspawn); the only way to permanently end the Blight is to kill the archdemon. Unfortunately, although Cailan is willing to take Duncan at his word, the Grey Wardens do not enjoy a good reputation in Ferelden: it has been over four hundred years since the last Blight and few are taking the possibility a new one has begun seriously, the Grey Wardens have relatively few numbers in Ferelden (two hundred years ago, they were exiled for participating in a revolt to overthrow a tyrant king of Ferelden, only being allowed to return twenty years earlier by King Maric, Cailan's father), and most of those are from the neighbouring kingdom of Orlais, whose brutal, century-long occupation of Ferelden (ended thirty years earlier by Maric and Loghain) is still a bitter subject for many.
Duncan orders the new Warden and Alistair, along with two other potential recruits, to go into the forests around the fortress to retrieve vials of darkspawn blood for the Joining, an initiation ritual that will induct the new recruits into the Grey Wardens, as well as treaties housed in an abandoned fort nearby that compel certain organisations to render aid to the Grey Wardens during a Blight. The treaties are not in the fort however, but a young witch by the name of Morrigan prowling the site brings the Wardens to her mother, a powerful sorceress called Flemeth, who took the scrolls for safe-keeping.
Returning to Ostagar, Duncan explains that the Joining involves drinking darkspawn blood, which will either kill the drinker (as it is highly poisonous) or will grant them the ability to sense darkspawn and a rudimentary connection into their hive mind. The player's character is the only one to survive the ritual, after which they and Duncan attend a war council to discuss strategy for the coming battle. Since Loghain will not hear of waiting for reinforcements the Grey Wardens of Orlais are bringing across the border to support their Fereldan compatriots, he and Cailan settle upon another strategy: Cailan, along with Duncan, the Grey Wardens and a significant force of Ferelden's army will act as bait in the valley the fortress overlooks, to lure the darkspawn into attacking. The Warden and Alistair are charged with lighting a beacon at the top of Ostagar, which will signal Loghain to charge the darkspawn in the flank once they are engaged with Cailan's forces. In the battle that follows, when the signal is lit, Loghain instead betrays Cailan and quits the field with his army. Without reinforcements, the darkspawn massacre the forces in the valley; Cailan, Duncan and the Grey Wardens are all killed.
The Warden and Alistair are rescued from death by Flemeth, who takes them back to her home in the forests. She urges them to use the treaties to raise a new army to replace the one destroyed at Ostagar, as if the Blight is not stopped soon, the darkspawn will destroy Ferelden and then spread to other regions. Flemeth offers Morrigan's services to them, insisting they can use her help, then directs them to the town of Lothering, where they can learn what is happening and determine their best course of action. Simultaneously in Denerim, Ferelden's capital city, Loghain presents his own version of what happened at Ostagar to the nation's nobility, placing blame for the disaster squarely on the Grey Wardens, before declaring himself regent to Queen Anora, his daughter and Cailan's widow. This move is met with outrage by the nobility, most of whom look down on Loghain as an upjumped commoner (though he is a war hero and veteran of Ferelden's war for independence from Orlais, he is a farmer's son and has no legitimate claim to the throne) and see his taking the regency as a blatant grab for power, and his dismissal of their concerns sow the seeds of civil war.
The Warden and their companions arrive in Lothering to find it in disarray: the vanguard of the darkspawn horde are only days away, and bandits and criminals are preying on those trying to flee for their lives. Gathering supplies and information before heading on, the group have the opportunity to add new companions to their ranks; Leliana, a sister of the Chantry in Lothering, who believes she has been divinely called to combat the Blight, and Sten, a warrior of the northern people known as the Qunari, who has been ordered to fight the Blight by his superiors and seeks to atone for crimes he has committed. The party then depart Lothering to track down the four groups who they can call upon to raise an army:
- Alistair suggests seeking aid from Arl Eamon Guerrin, the elder of King Cailan's maternal uncles and a popular man amongst Ferelden's nobility. As his forces did not fight at Ostagar, his army remains the largest not sworn to Loghain. Unfortunately, Eamon has been struck down by a strange and mysterious illness that defies all efforts to heal it. The Arl's pious wife, Lady Isolde, is convinced the only thing that can save her husband now is the Urn of Sacred Ashes, a container for the mortal remains of Andraste, the Chantry's messianic figure, said to have incredible healing powers, and implores the Warden and their company to find the Urn.
- The Circle of Magi, a Chantry-operated organisation that monitors and polices the use of magic, have long aided the Grey Wardens in the Blights. However, upon arrival at the Circle's stronghold in Ferelden, the Wardens discover an insurrection has taken place; mages in league with Loghain tried to convince the Circle to back Loghain's claim to the regency, but when others revealed his treachery at Ostagar, a battle broke out between both sides, and in the chaos, legions of demons were let loose, killing many and possessing others. The Warden must work quickly to put an end to the disaster, if they are to ensure the Circle's magic will be at their side against the darkspawn.
- The Dalish elf clans, nomadic survivors of the long fallen elven empire, have little love for the kingdoms of humanity, but the darkspawn will not spare them either and they are compelled to aid the Grey Wardens against the Blight. Encountering a Dalish clan within the forests to the south-east of Ferelden, the Warden's party discover the elves are being attacked by werewolves, and many in the clan have been infected with lycanthropy. The clan's Keeper (a mixture of tribal chieftain and shaman) Zathrian, requests the Warden bring him the heart of the werewolves' leader, as it will allow him to cure the afflicted, but as they venture into the forests, the Wardens discover that the werewolves seek redress of an ancient wrong done to them by the elves, and the Warden must decide whose side they will take in a bitter dispute spanning centuries.
- With the death of their king Endrin Aeducan, the dwarves of the city of Orzammar are in disarray as bitter infighting over who next takes the throne rages, while criminal elements in the city are taking advantage of the chaos to enrich themselves. The Warden finds themselves forced to side with one of the two candidates for the dwarven throne; either Lord Pyral Harrowmont, the late King's chief advisor, said to be a good man but one devoted to the conservative traditions of the dwarves, or Prince Bhelen Aeducan, King Endrin's last surviving son, who favours change and wants to advance Orzammar's society, but is regarded with suspicion due to rumours he arranged the assassination and disgrace of his elder siblings to advance up the line of succession. After helping their chosen candidate amass political and popular support while restoring law and order to Orzammar, the Warden is asked to complete one final task to swing the balance completely in their candidate's favour: with the dwarven Assembly deadlocked, the only one who can sway the debate is a woman called Branka. A Paragon of the Dwarves, recognised for her genius and abilities so highly she is the closest thing the dwarves have to a living god, if Branka were to return and give her backing to one candidate or the other, the dwarves would be obliged to accept her choice. Unfortunately, Branka is gone from the city; two years earlier, she departed into the Deep Roads, a network of continent-spanning underground tunnels that once allowed the dwarves to traverse the length and breadth of Thedas, now long since abandoned and overrun with darkspawn, in search of some ancient dwarven artefact, and while most in Orzammar assume she's long dead, the stakes are now too high to simply take that as fact. The Warden, accompanied by Branka's ex-husband, the dwarven warrior Oghren, must journey through miles of hostile territory to find Branka and convince her to return and give her blessing to allow the dwarves a new king.
Once all these allies have been gathered, the Warden returns to Redcliffe to find that concurrently to their quest, Ferelden has collapsed into civil war. Loghain, convinced the Blight is a hoax to allow a new Orlesian invasion of Feredlden, has refused to resign the regency despite the accusations of his involvement in Cailan's death and the Fereldan nobility's refusal to bow down to his authority has caused a civil war. Even worse, the darkspawn have taken advantage of the chaos to advance further into Ferelden unopposed. At this time, Eamon and Alistair reveal a secret; Alistair is a bastard son of King Maric, King Cailan's half-brother. He was raised by Eamon away from court to stop Cailan's enemies using him as a pawn, but with Cailan dead, Alistair possesses a better claim to the throne of Ferelden as a blood son of King Maric than Queen Anora, Loghain's daughter and Cailan's widow. Eamon proposes a Landsmeet, a political gathering of all Ferelden's nobility in the capital city, Denerim, where they can put forward their case to dethrone Loghain and place Alistair on the throne.
Upon arrival in Denerim and after a brief attempt by Loghain to intimidate them into submission, the Warden is discreetly contacted by Erlina, a handmaiden of Queen Anora herself. The Queen has come to suspect her father's role in her husband's death, and fearing Loghain's pigheaded stubbornness will leave Ferelden defenceless against the darkspawn horde, is willing to offer an alliance to stop her father. At present however, Loghain's chief lieutenant, Arl Rendon Howe, is keeping her as a virtual hostage at his estate in Denerim, and Anora believes Howe, with her father's consent, plans to assassinate her and pin the killing on Eamon and the Warden to destroy their credibility at the Landsmeet. Given the seriousness of that threat, and the fact Anora could be an invaluable source of information on Loghain, the Warden and their companions mount a rescue mission. In the course of rescuing Anora, killing Howe along the way, the Warden can free a number of prisoners whose testimony would prove damning to Loghain at the Landsmeet. Among them is an Orlesian Grey Warden called Riordan, who was sent to investigate what was going on after Ostagar and why Loghain was blaming the Grey Wardens for the disaster.
Back at Eamon's estate, the Warden must make a choice who they will back; Anora is willing to support the Warden and Eamon against her father, but makes it clear her support is conditional on them backing her claim to the throne. The two claimants for the throne have both good and bad points; Alistair has little experience with politics and ruling, but he is a good man willing to learn, and with the right guidance and direction could become a good king in time. Anora, on the other hand, is an experienced politician and diplomat, having been Ferelden's de facto ruler for years, but like her father, she is proud, stubborn and arrogantly overconfident in her abilities, and the fact she was never able to give Cailan a child cast serious doubts about her ability to continue the royal line. Anora does however provide the Warden with information regarding potentially damning acts and practices Loghain has condoned amongst his forces that would help shatter his credibility at the Landsmeet. Once they have completed their investigations, the Landsmeet begins in earnest; Loghain continues to blame the Grey Wardens for the defeat at Ostagar and being facilitators of a new Orlesian conquest of Ferelden, while the Warden argues the severity of the threat posed by the Blight and lists the atrocities Loghain has committed (including torture, assassination, murder, endorsing slavery) in a bid to retain a throne he has no right to. Whether by political means or direct force, the Landsmeet turns against Loghain and strips him of his power and authority, leaving his fate in the hands of the victorious Warden.
The Warden must now make a choice; Anora wants her father spared, both out of paternal loyalty and because of his years of previously loyal service to the nation, while Alistair wants the man whose treachery cost his half-brother, his mentor Duncan and his friends in the Grey Wardens their lives executed. Riordan offers a compromise between both sides in putting Loghain through the Joining; if he dies in the ritual, justice is served for his crimes, and if he lives, the Grey Wardens gain a skilled military commander to their ranks. The Warden must decide Loghain's fate and the matter of who takes the throne of Ferelden in Cailan's place (either Alistair or Anora rules alone, the pair join together in a political marriage, or a Human Noble Warden can arrange matters to rule besides them- a male Warden can rule besides Anora as Prince Consort, while a female Warden can wed Alistair and become his Queen, though this is dependent on certain conditions- if Loghain is executed, Anora will refuse to wed her father's killer, and if he is spared, Alistair leaves the party in disgust).
Once the matter is done, the Warden and their companions head back to Redcliffe, where the darkspawn are rumoured to be moving to attack. However, after fending off an attack on Eamon's castle, they discover from Riordan they have been duped; contrary to what all their intelligence suggested, the bulk of the darkspawn horde has circled around them and is now moving to attack Denerim. With most of its soldiers having gone to reinforce Redcliffe, the capital city is all but defenceless and to make matters worse, the archdemon itself is personally leading the attack. The gathered forces decide to make a forced march back to Denerim; if they can kill the archdemon before it and its army move on from sacking the city, they can end the Blight before it spreads beyond Ferelden. In private, however, Riordan explains why the Grey Wardens are essential to stopping the Blight; while archdemons are not invulnerable, if an ordinary warrior strikes a fatal blow against the dragon, its spirit will survive its body's death and find a new host in the nearest darkspawn, making the archdemon effectively immortal. If a Grey Warden deals the killing blow however, the archdemon's spirit will be drawn into the Warden's body, killing them both. Riordan is willing to make that sacrifice, but warns the other Wardens they must be prepared to do the same if needs be.
It is after this meeting that Morrigan confronts the Warden in their chambers and offers an alternative: a magical ritual that involves a Grey Warden conceiving a child with her. The child will possess the taint and at such an early stage in its development, absorb the archdemon's spirit without perishing, ending the Blight but sparing the Grey Warden the need to die to do so. In return, Morrigan gains a child born with the soul of an Old God, effectively a demi-god that she intends to raise by herself for her own ends (Morrigan freely admits this has been the sole reason she accompanied the Wardens, and the sole reason Flemeth saved their lives at Ostagar). The Warden can either sleep with Morrigan or, if they are unwilling or female, convince Alistair or Loghain to do it. If her offer is refused, Morrigan leaves.
The Wardens and their army march to Denerim and a bloody battle ensues between the forces they have gathered and the darkspawn rampaging through the city. In the course of the battle, Riordan is able to cripple the archdemon to stop it escaping Denerim, though doing so costs him his life. Fighting their way through the city, the Warden confronts the archdemon at the summit of Fort Drakon, a fortress that is the tallest building in the city, and after a climactic final battle against the archdemon and the darkspawn trying to defend it, brings the dragon down. If the ritual with Morrigan is performed, the Warden automatically deals the fatal blow; if not, they must decide whether they or their companion will sacrifice their life to kill the monster. Either way, the archdemon is slain, and the darkspawn horde, robbed of the will to fight on without their leader, retreat from Denerim in disarray, bringing the Fifth Blight to an end.
The story concludes with the new monarch of Ferelden being crowned, the Warden and their companions being honoured for their bravery in fighting the Blight and an epilogue detailing the consequences of the Warden's choices over the course of the story for Ferelden and Thedas.