Before the Landsmeet, Isabel tells Anora that Alistair wants Loghain dead and that she’s not going to stand in the way of that since he didn’t stand in the way of her revenge with Howe. It’s not the best political move on her part (she should really know better since she’s very good with this stuff), but she’s 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 Eamon’s 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 it’s what Duncan would do, and that killing Loghain won’t bring Duncan back, that she’s doing this to protect him, etc. Alistair threatens to leave, and Isabel snaps at him and tells him that he can’t because Anora would have him killed (I am fully aware you can convince her to let him live, but Isabel doesn’t know this at the time because again, she’s not thinking straight thanks to the threat on Alistair’s life). He gets even more angry and snaps back at her, saying he’s stuck taking the throne and that it’s better off that way because he’s not going to be a Warden with Loghain.
Eamon interrupts them, because they’re 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 Eamon’s troops left for Redcliffe and that he’s going to remain in Denerim since he’s stuck being the king now. They end up arguing some more–she says he can’t just leave the Wardens and that he can’t leave her, he’s super pissed and accuses her of some pretty bad things–and Alistair essentially breaks up with her.
Isabel is devastated and ends up crying herself to sleep in Wynne’s arms that night. Wynne gives Alistair a stern talking to about how he’s making an epic mistake and that he was foolish to throw away what they had just because he disagreed with what she did–which was to protect him in the first place. Alistair ends up going along with them to Redcliffe, claiming that if he’s going to be king he has to be with his troops, when in reality Wynne’s words got to him and he’s 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 doesn’t like it and doesn’t want anything to do with Loghain. They make up and he ends up awkwardly proposing to her: Isabel makes sure that he’s really okay with being king and he says he’s 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 Morrigan’s description has appeared again, she has her spies gather as much information as they can about the mysterious woman.
When she’s positive it’s Morrigan, she asks Nathaniel Howe to search for her. She had previously named him Warden-Commander after the events of Awakening, and since she’s 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 she’s done for her before Morrigan finally leaves.
She does not “vanish.” When Morrigan resurfaces and contacts her about a lead on a possible cure to the Calling, she sends Nathaniel Howe to search for it. (It’s the same situation as in Witch Hunt: he’s still technically a Warden since he’s the Warden-Commander and she trusts him with such a matter. She’s 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 can’t afford to leave for a lead that might not work out.)
Cassandra does contact her about leading the Inquisition before she interrogates Varric about Hawke's whereabouts, but Isabel declines the offer. She can’t afford to leave Denerim for that long, and it wouldn’t be good for the Queen of Ferelden to be the head of a Chantry organization.
Shortly before Inquisition begins, she and Alistair start to hear the false Calling—it terrifies them, until they learn it’s not real.
She accompanies Alistair to Redcliffe and they meet the Inquisitor after 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 for Here Lies the Abyss through Leliana, and actually goes to Loghain in order to help him and find out why she lost contact with him for so long. She’s actually in Crestwood when the Inquisitor 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 Leliana’s agents helps drive them out (the Shadows Over Denerim 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 (the Delicate Negotiations 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.
