The central character, Kira, who has a deformed leg, is recently orphaned (her mother abruptly dying from unknown sickness, and her father years past dying while on a hunt with all the Hunters, being killed by The Beasts) and must learn to survive in a society that normally leaves the weak or disabled exposed to die in the fields.
In Gathering Blue, Kira needs a reason for the Council of Edifice to keep her in the village and not take her to the Field (which is certain death at the hands of The Beasts). A member of the Council named Jamison defends Kira during the trial - much to Kira's surprise. He argues that he knew Kira's dad, and that Kira has a gift for embroidery. The Council decides to keep her around to mend and update a beautiful robe that shows the history of their society. The robe is only worn at The Gathering, a yearly event that brings the entire civilization together. Someone designated as the Singer wears the robe and sings a lengthy song telling the history of man, in order to remind the citizens of the rise and fall that occurs due to imperfection. As such, Kira leaves the slums and poor conditions she is used to, and is taken to live in a beautiful and comfortable room within the same building she remembered standing on trial.
She is taught how to further solidify this talent from a much older woman named Annabella. Annabella continues to teach Kira how to create dyes for different shades and hues for her threadwork. To Kira's dismay she learns that there is no ability to create the color blue for the threads she will be using. Eventually, to Kira's surprise Annabella tells her that with her own years and knowledge, she knows much of the society's history, even going so far as to say that there really are no Beasts, as the society teaches. Kira doesn't know what to think of this, nor what Annabella really means by it.
Along the way she becomes closer friends with a younger boy named Matt, and also makes a new friend in her neighbor at her new home: Thomas. Thomas is a boy around Kira's age, who is also an orphan. Thomas has lived there since he was very young, because of his abilities. It is learned that he is the woodworker that maintains and improves the Singer's staff - which in turn helps the Singer remember the history of the society as he sings the lengthy song. Together they help each other bring out the best in their talents, preparing for The Gathering. Jamison, the Guardian who fought for her life in the trial becomes somewhat of a mentor in her new home. He is kind, and instructive, yet also very stern.
Kira slowly learns that her life is less than idyllic. Thomas hears crying in her building, and she and Thomas discover another orphan, a very young girl named Jo, whose ability to sing is magnificent; she is kept with intent to eventually replace the current Singer. Jo is scolded and punished if she does not sing; Kira secretly befriends her, (sneaking into Jo's locked room at night to comfort her) and realizes that she, Thomas, and Jo do not have as much freedom as they had previously thought. Annabella abruptly dies, and Kira is left to continue her work. This and the secluded life that a very young Jo must live, help Kira decide to find out the truth about her society.
On the day that the Singer sings the Song at the Gathering, Matt is nowhere to be found. At the Ceremony of the Gathering, she notices that the current Singer has the staff that Thomas has worked so hard on; and is also wearing the robe that she repaired, and enhanced. She realizes that his feet are chained, injured, scarred, and bleeding; meaning that he is essentially a prisoner, only kept for this one event because of his talent. The implication is that she and the others with Gifts, that the Counsel has saved for these jobs are also prisoners. Their gifts are in control of the Counsel, by tenants who without any creativity of their own seek to control these three, in order to provide a future which they want.
Matt after a long absence returns with a blind man from a distant village called the Village of Healing. The man is interestingly enough wearing a blue shirt - something that Kira's people don't do due to the lack of knowledge thereof. It turns out that he is the father who Kira thought was dead: Christopher. It is revealed that he had been attacked by another hunter years before who was jealous of his immediate potential of being a member on the Counsel of the Guardians. First, he was beaten and then by knife to his face - he lost his sight. Being taken to the fields to die amongst the other rejected ailed, injured, and dying citizens of their society, he was rescued by some people he could not see - who took him to the Village he now lives in. The community in which he now lives is made up of injured and disabled people who help one another, rather than bicker and fight for their lives as Kira's does. Matt excitedly explains that in this Village they know the way to make blue threads, bringing plants that will allow Kira to do the same.
After a long heartfelt reunion with his daughter, Christopher reveals that he has enemies on the Counsel. The one who maimed him years before was none other than Jamison. He tearfully apologizes for taking so long to return to get her; because of his memory loss caused by the beating, and his loss of sight - he had no way of finding her. It was because Matt had gone looking for a way to make blue for Kira, and stumbled upon Christopher's Village, explaining where he came from - that the events began to roll forward in such a way that Christopher could again reunite with his daughter. Kira begins to wonder if her mother's sudden death, as well as the deaths of the two other orphans' parents, were actually at the hand of the Counsel; in order to acquire these young, gifted children - seeking to mold them into creating the future which they want.
Christopher cannot stay and is forced to return, while Kira decides to stay in her own community to continue to embroider the Singer's robe and help improve the society she lives in. Matt is designated as the 'eyes' that will help Christopher find his way back. It is implied that Thomas, Kira, and Jo - being the new holders of the Gifts - have the opportunity to change the cycle of their society and vastly improve the conditions in which they live, by using their gifts to influence the actions of their people.
During the end of the book Matt tells Kira that in the Village which he visited all are important, and all are married (something she would have to do without in her current society, seeing as the injured and impaired are seen as worthless wastes of space). He continues to tell her about a boy from Christopher's Village. He says the boy has blue eyes, is around her age, and is not injured in any way (referencing Jonas from The Giver); hoping that this will entice her to come with them. Kira declines to go with them to the new Village, but it is decided that she will eventually follow once her work in in her current task is finished. In the meantime, Matt will travel back and forth between Kira and her father Christopher, being called their Messenger, relaying their messages.