The series contains seven books focusing on the conflict caused Quill, an oppressive dictatorship ruled by the High Priest Justine, where creativity and independent thought is banned and people are classified into three tiers: Wanteds, Necessaries, and the titular Unwanteds.
The series is mainly told from the perspective of Alex Stowe, who was framed for an act of creativity by his twin brother Aaron (a minor narrator) after he drew in the mud as a child. Since Aaron escapes the situation and leads an otherwise model life in Quill, he is deemed to be Wanted while Alex is classified as Unwanted in the annual Purge. Supposedly, Unwanteds are executed in the lake of boiling oil (an unexplained location), but to the group's surprise they are saved by the eccentric Marcus Today (who is otherwise referred to as Mr. Today).
Marcus Today is the twin brother of Justine, and can be considered her opposite. Today takes the Unwanteds to a hidden land referred to as Artimé (who's existence is sustained by the Head Mage's robe), where the children's creativity is channelled into magic. Following Today's death, Alex unintentionally becomes Head Mage after figuring out how Today used the robe. The series follows his exploits in that position while Aaron carries out a subtle yet persistent campaign to install himself as High Priest, eventually succeeding.
The series concludes with the unification of Artimé and Quill, and is followed by a spin-off series entitled The Unwanteds Quest.