As the most recent recruit of Ferelden's Grey Wardens, Alistair helps the Warden prepare for their Joining at the fortress of Ostagar. He accompanies the Warden into the Korcari Wilds as part of their pre-Joining trials, encountering the apostate, Morrigan there along with her mother, Flemeth, both of whom Alistair distrusts.

Following the latter's successful Joining, Alistair and the Warden are given the task of lighting the beacon atop the Tower of Ishal. The tower is crawling with darkspawn by the time the pair reach it, and though they successfully fight their way to the top and light the beacon, Loghain Mac Tir, teyrn of Gwaren and leader of King Cailan's armies, abandons his king and retreats. Alistair and the Warden are overwhelmed by darkspawn and would have perished, but are saved by the intervention of Flemeth.

Alistair is nursed back to health by Flemeth and Morrigan and is utterly devastated to hear of the defeat at Ostagar and Duncan's death, laying the seeds for a passionate hatred of Teyrn Loghain. Following their recovery, Alistair and the Warden set out to rebuild the army lost at Ostagar and defeat the Blight. Upon their approach to Redcliffe, Alistair reveals the truth concerning his parentage. With the downfall of King Cailan at Ostagar, Alistair's bloodline means that he is the last of the Theirin bloodline, and a claimant to the throne.

Alistair longs to be reunited with Goldanna, the woman he believes to be his half-sister. With the aid of the Warden, Alistair eventually tracks Goldanna down, discovering that she is living as an impoverished washerwoman in the capital. Alistair's familial affection for his half-sister is not mutual, with Goldanna harboring a deep resentment toward what she perceives as Alistair's privileged upbringing and her belief that he had killed their mother.

If Alistair remains unhardened:

Alistair's hopes of a joyous meeting with Goldanna are quashed, leading him to put thoughts of his family aside and continue in his quest. Alistair's experience with his half-sister does not dramatically affect his personality, however, remaining relatively idealistic and passive.

If Alistair is hardened:

Following his disastrous encounter with Goldanna, Alistair is chastised by the Warden for being too passive in his interactions with others. This leads Alistair to become much more assertive, taking a considerably more pragmatic approach to problems, in contrast with his formerly idealistic outlook. After finally reaching the Landsmeet, Alistair participates in laying the cause against Teyrn Loghain before the nobility of Ferelden. Loghain is finally defeated by force of arms and is about to be executed, but the execution is halted by the intervention of the senior Grey Warden Riordan, who suggests that instead of wasting his life, Loghain should undergo the Joining ritual and join the ranks of the Wardens. If Alistair was chosen to duel Loghain, Loghain is content that there is still some of Maric in him after being defeated. Alistair dismissed Maric's relevance to him and performed Loghain's execution to avenge Duncan without hesitation.

If Alistair is executed:

Riordan's compromise is accepted by the Warden, Queen Anora and Loghain himself, though Alistair refuses to countenance it. After being declared queen by the Landsmeet, Anora orders Alistair's execution.

If Alistair becomes a drunk:

Loghain's admission to the Wardens' ranks is agreed to, though Alistair becomes enraged at this suggestion. He issues an ultimatum, threatening to leave the Wardens if Loghain is not executed. Though Queen Anora demands Alistair's life, he is allowed to leave the Landsmeet alive. He abandons the Grey Wardens and becomes a roving drunk, wandering from tavern to tavern and eventually travelling across the Waking Sea to Kirkwall.

If Alistair marries Anora and Loghain lives:

Alistair is infuriated that Loghain has been permitted to join the Wardens, prompting him to leave their ranks. He nevertheless fulfills his birthright and accepts the crown, marrying and ruling jointly with Queen Anora.

If Alistair marries Anora and Loghain dies:

Alistair's wish is fulfilled as Loghain's execution is carried out in the Landsmeet. Alistair and Anora had reluctantly agree to marry, and so are declared co-monarchs of Ferelden by the Landsmeet.

If Alistair marries the Warden:

Loghain is beheaded for his crimes, though the issue of Ferelden's vacant throne remains unresolved. The Warden takes up the role of kingmaker, crowning Alistair king and unexpectedly announcing that the Warden will rule beside him as his wife and queen. Alistair is surprised at this conclusion but does not object.

If Alistair is made sole king:

Following the execution of Teyrn Loghain, The Warden resolves the issue of the vacant throne of Ferelden by declaring Alistair to be king, his Theirin blood giving him the strongest claim. On the advice of Arl Eamon, Alistair imprisons Anora after she refuses to swear an oath of fealty to him. His first act as king is to appoint The Warden as leader of the Fereldan Coalition but he will continue to serve the Grey Wardens until the Fifth Blight is defeated.

If Alistair remains a Grey Warden:

Loghain is executed during the Landsmeet though the crown passes over Alistair as Anora is declared queen. Alistair is content to remain a Warden and not be burdened by royal duties. Alistair participates in the relief of Redcliffe, which has been attacked by a host of darkspawn. He later makes preparations with the Warden, Arl Eamon, Bann Teagan and others to march on Denerim and vanquish the Blight at last.

If Alistair makes the ultimate sacrifice:

Atop Fort Drakon, Alistair plunges his blade into Urthemiel, giving his own life to end the Blight. He is remembered as a hero by the people of Ferelden.

If Alistair became the sole King of Ferelden he will still offer to make the ultimate sacrifice calling it "His first and last act as King". If King Alistair dies, Anora will become the new Queen and in her speech will mention that the Theirin bloodline died with Alistair.

If Alistair completes the Dark Ritual:

Following the revelation that the sacrifice of a Warden's life is necessary to slay the Archdemon, Morrigan offers an alternative: by participating in a mysterious ritual, a Warden could father a child with Morrigan and thus kill the Archdemon without making the ultimate sacrifice. Alistair is persuaded to participate in this ritual despite the animosity between him and Morrigan. This saved both his and The Warden's life, and they defeat the Archdemon and are hailed as heroes.