Before the Landsmeet, Isabel tells Anora that Alistair wants Loghain dead and that sheās not going to stand in the way of that since he didnāt stand in the way of her revenge with Howe. Itās not the best political move on her part (she should really know better since sheās very good with this stuff), but sheās not exactly thinking straight throughout the whole Landsmeet. Naturally, Anora rightfully sides with her father in the Landsmeet, and her vote ends up breaking a tie between the nobles.
Loghain calls for Isabel, Alistair, and Eamonās executions for treason, a fight breaking out as they try to defend themselves until the Grand Cleric proposes a duel. Alistair and Loghain duel and Alistair just barely manages to win and is completely ready to kill Loghain. When Riordan proposes that Loghain join the Wardens, Isabel agrees, and Alistair claims the throne because he sees it as the only way to get justice for Duncan.
Isabel pulls him aside to speak privately, and they get into an argument. Isabel believes Riordan is right and that they need Loghain. She tells Alistair that itās what Duncan would do, and that killing Loghain wonāt bring Duncan back, that sheās doing this to protect him, etc. Alistair threatens to leave, and Isabel snaps at him and tells him that he canāt because Anora would have him killed (IĀ am fully aware you can convince her to let him live, butĀ IsabelĀ doesnāt know this at the time because again, sheās not thinking straight thanks to the threat on Alistairās life). He gets even more angry and snaps back at her, saying heās stuck taking the throne and that itās better off that way because heās not going to be a Warden with Loghain.
Eamon interrupts them, because theyāre standing there arguing like children in front of the entire Landsmeet, and he says that the matter is settled and that Alistair will be taking the throne since he won the duel and all that. Alistair makes his speech, Anora is imprisoned (she is released after the Blight and is given Gwaren), and Loghain goes off with Riordan to go through the Joining.
The Landsmeet disperses and Eamon drags Alistair away to discuss kingly things. Afterwards, Alistair finds Isabel and tells her that Eamonās troops left for Redcliffe and that heās going to remain in Denerim since heās stuck being the king now. They end up arguing some moreāshe says he canāt just leave the Wardens and that he canāt leave her, heās super pissed and accuses her of some pretty bad thingsāand Alistair essentially breaks up with her.
Isabel is devastated and ends up crying herself to sleep in Wynneās arms that night. Wynne gives Alistair a stern talking to about how heās making an epic mistake and that he was foolish to throw away what they had just because he disagreed with what she didāwhich was to protect him in the first place. Alistair ends up going along with them to Redcliffe, claiming that if heās going to be king he has to be with his troops, when in reality Wynneās words got to him and heās just not ready to stop being angry yet.
After all the time on the road between Denerim and Redcliffe, he comes to understand why Isabel did what she did, even if he doesnāt like it and doesnāt want anything to do with Loghain. They make up and he ends up awkwardly proposing to her: Isabel makes sure that heās really okay with being king and he says heās good. He mentions that Eamon babbled about finding him a suitable queen and that all he could think about was marrying her even though he was royally pissed off at her.
So there you have it, Alistair ends up as king and Isabel eventually marries him and becomes queen, and Loghain is still alive and a Warden.
When Isabel hears whispers that a woman matching Morriganās description has appeared again, she has her spies gather as much information as they can about the mysterious woman.
When sheās positive itās Morrigan, she asks Nathaniel Howe to search for her. She had previously named him Warden-Commander after the events of Awakening, and since sheās stuck in Denerim ruling with Alistair, she needed someone she trusted to look for her, and that person was Nathaniel.
Nathaniel keeps Isabel informed of everything he finds as he searches for Morrigan.
Before she enters the Eluvian and disappears, Morrigan ends up quickly stopping by the palace to see Isabel one last time. She informs her about the Eluvian, Flemeth, etc., and Isabel says goodbye to her friend, thanking her for everything sheās done for her before Morrigan finally leaves.
She does not āvanish.ā When Morrigan resurfaces and contacts her about a lead on a possible cure to the Calling, she sends Nathaniel Howe to search for it. (Itās the same situation as in Witch Hunt: heās still technically a Warden since heās the Warden-Commander and she trusts him with such a matter. Sheās also extremely busy in Denerim ruling with Alistair and trying to keep the country together as the world is starting to fall apart, so she canāt afford to leave for a lead that might not work out.)
Cassandra does contact her about leading the Inquisition before she interrogates Varric aboutĀ Hawke'sĀ whereabouts, but Isabel declines the offer. She canāt afford to leave Denerim for that long, and it wouldnāt be good for theĀ Queen of FereldenĀ to be the head of aĀ ChantryĀ organization.Ā
Shortly before Inquisition begins, she and Alistair start to hear the false Callingāit terrifies them, until they learn itās not real.
She accompanies Alistair to Redcliffe and they meet theĀ InquisitorĀ afterĀ In Hushed Whispers. While there, she and Alistair also question Fiona about the cure to the Calling.
Isabel gets the Inquisition in contact with Loghain forĀ Here Lies the AbyssĀ through Leliana, and actually goes to Loghain in order to help him and find out why she lost contact with him for so long. Sheās actually in Crestwood whenĀ the InquisitorĀ and her companions show up with Hawke to question Loghain, and ends up running around Crestwood with them for a bit.
Isabel and Alistair contact the Inquisition for help when they believe the Venatori have a presence inside the palace, and one of Lelianaās agents helps drive them out (theĀ Shadows Over DenerimĀ war table operation). Afterwards, they send Fereldan troops to Skyhold to assist the Inquisition.
Isabel, Alistair, and Celene send representatives to the peace talks in Jader, where a temporary peace agreement is signed (theĀ Delicate NegotiationsĀ war table operation). They all meet in person at Skyhold after Corypheus is defeated, where they agree to an official peace treaty between Ferelden and Orlais.
