History in Show
During his school years at Brakebills, he became friends with Emily Greenstreet and the two spent much time together. Emily attempted a dangerous spell to become more beautiful in order to win back the attentions of Professor Mayakovsky. However, spells to physically alter the body are very complex and Emily disfigured herself in the process. Charlie, seeing what Emily had done to herself, tried to reverse the damage. Despite Emily's pleading to stop, Charlie kept going and was consumed by magic entirely, transforming into a Niffin. Emily's face was then fixed by Mayakovsky and she gave up magic leaving Brakebills forever. Because Charlie's death was covered up, his younger sister snuck into Brakebills for the entrance exam to gain access to the school and figure out what happened.
Charlie was then summoned by Alice, who was determined to transform him from his niffin state back into his human form, but could not handle her brother's powerful magic. To save her, Quentin bound him into a box, locking him away for good.
History in Books
Charlie Quinn was the older brother of Alice. He was a student of Brakebills. Grossman doesn't literally say the precise cause of his death but it is assumed that he turned into a niffin. In the 'The Magicians' Janet tells the Physical Kids a story about the first girl who left Brakebills voluntarily, Emily Greenstreet. The story says that Emily used to date a Brakebills professor. When the professor stopped dating her she got mad. A boy who was in love with Emily tried to console her. Emily decided to use magic to make herself more beautiful. The boy helped her cast this magic but due to a mistake the boy turned into a niffin. The professor who dated Emily was given two options - to leave Brakebills with disgrace or Be a professor at Brakebills South in Antarctica. After the narration of the story by Janet, Alice becomes sad and leaves. When Quentin asks her the cause of her unhappiness she responds that the story was true and the boy who loved Emily Greenstreet was her brother Charlie Quinn as the occurrence of both the events - Charlie's death and Emily's departure - match. The professor who dated Emily is supposedly Professor Mayakovsky who is current professor of Brakebills South. When Alice became human after seven years of life as a Niffin she tells Quentin she looked for her brother everywhere but couldn't find him.
Deceased (Supposed Niffin)
Charlie was a nice and friendly guy, always ready to help his friends. Whenever his sister Alice was down in the dumps, he always knew how to make her laugh. Following his transformation into a Niffin, Charlie's Shade was lost and when summoned by his sister, expressed no empathy and attempted to kill her.