Maric is approached by Genevieve, Commander of the Grey Wardens in Orlais. Genevieve's brother, Bregan, has been captured by the darkspawn and, she believes, is being held near Ortan Thaig. Since Bregan knows where the Old Gods are buried, Genevieve fears that if the darkspawn gain this knowledge, they will use it to trigger a Blight in Ferelden. Maric and Loghain are the only two living people to have ventured that way and Maric, tired of the responsibilities of rule, despondent after the death of his wife Rowan, fleeing from what he sees as his failure as a father to his son, Cailan, and remembering a warning given to him by a mysterious witch of a Blight coming to Ferelden, Maric volunteers to guide the Grey Wardens into the Deep Roads. Thus he comes to travel with a band of Wardens including a young Duncan and an Orlesian elven mage named Fiona and to confront The Architect, an unusually intelligent darkspawn emissary with a very disturbing plan.

Bregan ventured into the Deep Roads after hearing his Calling. However, he knows the location of the Old Gods, which The Architect claims to want to locate and destroy to free the darkspawn from their siren call and ending the threat of future Blights. This, it claims, will facilitate peace between humans and the darkspawn but concluding such a peace would demand a huge price. The darkspawn taint turns creatures into ghouls, all except the Grey Wardens who are made, at least temporarily, immune to the taint by their Joining. Humans and darkspawn can only exists in harmony if the darkspawn taint is introduced to all humans across Thedas. With his mind disturbed by the encroaching darkspawn taint, to which his immunity is exhausted, Bregan falls in with The Architect's plans. It later transpires that The Architect also has other allies who cannot plead such an excuse, among them First Enchanter Remille of the Fereldan Circle of Magi.

The Grey Wardens and Maric venture into the Deep Roads and find Bregan and The Architect, but not before stumbling upon the horrors of the Deep Roads, with the group suffering many injuries and losing Nicolas and Julien (Julien is slain by a High Dragon, while Nicolas decides to stay behind in the Fade after they are trapped there by a demon). However, some trinkets given to the Wardens by First Enchanter Remille allegedly to prevent the darkspawn from sensing the Wardens have instead served to rapidly accelerate the progress of the taint in them. Only Duncan, protected by a dagger he stole from Remille, remains immune. The group are ambushed by the darkspawn and nearly killed, though the Architect manages to save and take them prisoner. Suffering, it is to be supposed, from the mental effects of the taint, Genevieve and the Silent Sister Utha agree to join Bregan and The Architect to destroy the Old Gods, though the full extent of The Architect's plans is not revealed to them.

The rest of the surviving Grey Wardens and Maric attempt to escape. Only Duncan, Fiona and Maric make it out of the Deep Roads (Kell and Hafter sacrifice themselves to buy the others time), and then only to find themselves tricked and captured by First Enchanter Remille and taken to the Circle Tower. There, they re-encounter The Architect, Bregan, Genevieve and Utha. It is revealed the Architect has made a deal with Remille, offering him knowledge of darkspawn magic to protect the people of Orlais from the taint and Maric as a captive for the Orlesian Emperor in exchange for the Circle's help in spreading the taint. However, the Architect's plans are thwarted when Loghain, having learned what is going on, arrives with an army to rescue Maric, and Bregan and Genevieve renounce The Architect's plans. They and the traitorous Remille are killed in the final showdown, but The Architect and Utha escape.