Act 1

Following the events surrounding the disappearance of Tamlen, Merrill has kept a fragment of the Eluvian in the old ruins to cleanse it of its taint. She studied the lore on the Eluvian, and extrapolated information from the shard.[4] Merrill asks Marethari for help in cleansing the shard of the taint, but the Keeper refuses.

Her efforts to construct an Eluvian – a combination of her ardent lack of interpersonal skills and her pragmatism – caused her to turn to blood magic, which she learned from a pride demon imprisoned and sundered from the Fade atop Sundermount. As she lacked the necessary amount of lyrium to cleanse the shard with ordinary magic, she used blood magic to amplify her power so she could succeed; this spell seemed to be utilized in the Dalish Origin to help the Warden deal with the taint. She argues with Marethari that her efforts to learn blood magic were necessary towards the restoration of the Eluvian, and ultimately the survival of the Dalish; with the Keeper publicly opposed to her efforts, the clan turns against her.

When Hawke arrives at the Dalish camp in Sundermount, she takes part in a ritual that Hawke is to perform on a mountain-top altar. In the rite, Merrill recites the song In Uthenera, a poem for the departed. The ritual entails the resurrection of Flemeth, as a portion of her essence is revealed to have been embedded in the amulet. Marethari explains to Hawke that Merrill had decided to leave her increasingly hostile clan to learn more about the outside world and continue her studies into restoring the Eluvian. Initially nervous when arriving in Kirkwall, Merrill finds lodging in the city's Alienage and joins Hawke's party. However, while staying in Kirkwall, her use of blood magic puts Merrill at odds with Anders and Fenris.

Act 2

Three years have passed since Hawke joined the voyage to the Deep Roads, and Merrill seeks Hawke's help in facing Marethari to request a special dagger to help complete the Eluvian. As they confront the Keeper, she calls upon vir sulevanan, the right of every Dalish to claim any property or artifact of the clan in exchange for a service. Reluctantly, Marethari requests that they slay a Varterral that had killed many of their hunters, as the deal for the dagger. While exploring the Varterral's lair, they run into Pol, who flees in fear at the sight of Merrill, straight to the Varterral itself. After killing the Varterral and returning to camp, Merrill inquires as to why Pol was so afraid of her. She discovers that Marethari had warned her clan that she might potentially bring back the darkspawn taint. Marethari tries to use this to coerce Merrill to abandon her research on the Eluvian, and return to the clan; Merrill adamantly refuses. Though Merrill honors her side of the bargain, the Keeper does not, and instead, gives it to Hawke for safekeeping, leaving Hawke with the choice to either give the Arulin'Holm to Merrill or deny her the tool.

Act 3

After another three years since the invasion of the Qunari, Merrill finds an alternative to fixing the still-inactive Eluvian, regardless whether Hawke gave the Arulin'Holm to Merrill or not. She plans to consult Audacity, who said to her years ago that he witnessed the creation of the mirror itself during the days of Arlathan. She asks Hawke to accompany her to Sundermount, as she is concerned about the threat Audacity may pose, particularly as it has been silent in her recent attempts to communicate remotely with it. It's discovered the Keeper released Audacity from its prison, and contained the demon within herself, independent of whether Hawke supports Merrill's plan or not. Marethari claims that the demon was intending to use the Eluvian as a way out of its prison and that Merrill would've been its first victim, but never explains how she came to this conclusion.

As an abomination, Marethari attacks Merrill and her companions, forcing them to kill her to survive. As Merrill mourns Marethari, Hawke can comment on the Keeper's recent actions, including informing Merrill that the Keeper "was stupid" for releasing Audacity. Afterward, the clan will confront and interrogate Hawke and Merrill about the Keeper's disappearance, eventually discovering that she is dead. If Hawke reveals the Keeper became possessed by the demon or warns the clan to back off, they will attack and force Hawke and Merrill to kill them to survive. However, if Hawke blames Merrill for Marethari's actions, the clan will only ask them to leave.

Back in the Alienage, Merrill is crushed. If she and Hawke are rivals, she bemoans that she was too "stupid and ignorant" to listen, then shatters the Eluvian. If they are on friendly terms, Merrill states that the clan and Keeper did not heed her when she was trying to help them, despite devoting several years of her life to helping end the plight of the People through the painstaking restoration of ancient elven technology that may have revitalized the People from their plight. She will consult Hawke on what should be her next course of action since the Eluvian remains inert.

Merrill pleads for Anders to be spared after he destroys the Kirkwall Chantry, and for him to assist the party and make up for his act. She willingly joins Hawke in defense of the mages. She can also stick with Hawke despite siding with the Templars, if completely loyal.

If otherwise, Merrill initially refuses to help a pro-Templar Hawke if she was not spoken to after an unpleasant encounter with her clan, and if Anders considers Hawke a full rival. He must also be talked with after fulfilling all his requests so that he can be potentially persuaded to turn against the mages; his actual fate is irrelevant.

Later, Hawke meets Merrill in the Gallows courtyard. If the Champion asks Merrill to rejoin them at this point, she can be convinced; Hawke is the only person she is very close with, a bond stronger than any she has with the Circle mages. Instead, if Hawke does not want Merrill at their side, she walks away to protect the Circle mages from the Rite of Annulment and is eventually killed in combat after her last words with Hawke.

If Merrill stands triumphant with Hawke after the battle in the Gallows, she leaves the Champion along with the others, for personal reasons, as stated by Varric