During her time in the Storytime, Zoe develops powers that she uses to help others lost in dreams and stuck in the dream world. She helps a woman who cannot stop falling, a man scared of the dark, and a child who thinks a monster in the wardrobe will eat her. In addition to convincing all of them to abandon the Dreammachine, she tells the man that he always had a light to banish the dark inside of him and there is no need to be afraid, and the child is convinced to stand up to her bully of a mother. Later Zoe meets the child who considers her a superhero.
Zoe refuses to believe the official stories about the deaths of Damien and Olivia, and how Damien took the blame for WATIcorp's Dreammachine fiasco.
Reza has stuck beside Zoe for a long time and still works exposing government corruption.
Though given that Reza's reintroduction at the end of Dreamfall was treated rather ominously and the fact that it's odd that Reza would simply believe Damien was responsible for the mind-control plot after working with him in trying to uncover the conspiracy before, it's possible he might not be as good as he seems, if he's not an outright villain.
Kian helps a dying man and has the ability to promise him that he'll try and find his children and tell them how much his father loves them.
The Warden tries to bond with Kian, and doesn't even like the fact that his execution is obviously a cover-up.
The Six, the leaders of the Azadi, apparently believe in Kian so much that the Governor of Marcuria, Sister Sahya, and Varmon have to kill Kian before one of them arrives, otherwise, his story will be believed by them. This is despite the fact that they know he is a traitor.
Magnus and Etta, Saga's parents, are deeply in love and care very much about Saga. Magnus has Etta's name tattooed in a heart on his bicep. In a game with very few positive relationships, it stands out.
Kian's "I'm doing this for April Ryan".
Mother Utana, when told by Sister Sahya that Kian was a traitor, cows with words alone and points out that Kian was never stripped of his title, and, without a proper trial, his treason was only an accusation.
Kian's interactions with Bip are nothing but adorable and aww-worthy, but one that stands out is the dialogue that results if you think to give Bip your sand-witch: Bip tells you he hasn't eaten this well since the last time his mom cooked for him.
This continues in Book 3, when Bip is abducted and taken to Ge'en, heavily implied to have become the Azadi version of a concentration camp.
We learn more of Anna's past, that she was rescued by Kian as a girl. It was the first time anyone had shown her kindness. While Kian does not remember it, it forged Anna to be a better person and fight to help others. Later, when Kian remarks that he never truly feels like a rebel, Anna remarks that Kian is who he has always been: Not an Apostle, or a rebel, but a man who helped others.
Zoe reunites with either KidBot or ShitBot, and is overjoyed to see them again.
Ferdows, the wimpy engineer who is lost in his pipes and tubes, becomes infuriated when he learns that not only are the magicals being killed, but they're hurting the children too. He fights off General Hami with no weapons at all, to allow Kian time to escape.
Crow reunites with Zoe, and, after some initial complaining, decides he wants to go on an adventure, even a dangerous one, with her again.
Near the end of Book 3, two Azadi soldiers are talking as Kian is trying to sneak onto the cloudship to rescue Bip from Ge'en. One of the soldiers is really upset about treating the magicals so badly, and remembers that he got great advice from a Dolmari farmer about growing technique. Even when his fellow Azadi berates him, the man refuses to see the magicals as less than people.
If you kept Na'ane's secret, she will use her medical skills and save Enu from death.
Hami fights to the death to save magicals. Many of his soldiers also convert to the rebels when they learn about Ge'en.
Saga saves Kian from death with her alchemy.
If she survived Book 4, Enu becomes a force of good that magicals and humans can respect in Marcuria.
At the epilogue, Kian can fondly pray for those who were lost, and hopes they find peace, or whatever they want that passes for it, in the afterlife.
Crow is savagely killed by Brian Westhouse, but there is a scene of him being reunited with his beloved April, and is overjoyed to go to the afterlife with her, on their next adventure. He is also somehow reincarnated by Saga, since a baby crow sits on her shoulder as she stands next to Kian, and as an old woman she has a very old crow as a companion.
Kian adopts Saga as his daughter. While things seemed rocky to begin with, it's clear that, at the end of time, a much older Saga remembers how much she loved him, and, in her centuries of life, didn't go one day without thinking about him.