Clary Fray is initially motivated by the mysterious disappearance of her mother, Jocelyn, and the strange visions she begins to experience. When she witnesses a murder in the Pandemonium Club and learns about the existence of the Shadow World, her determination to find her mother and uncover the truth about her family's past drives her deeper into this hidden realm.

Jace Wayland starts as a confident and skilled Shadowhunter, initially appearing aloof and somewhat arrogant. However, as he forms a bond with Clary, his character reveals deeper layers of vulnerability and complexity. He grapples with his feelings for Clary, especially when he learns about their potential familial connection, which complicates his emotions and motivations.

The Mortal Cup is a powerful artifact that can create new Shadowhunters by turning mundane humans into them. Throughout the film, it becomes the central object of desire for both the Shadowhunters and the antagonistic Valentine Morgenstern, who seeks to use it to create an army of Shadowhunters loyal to him. Clary's quest to find the cup is intertwined with her search for her mother and her understanding of her own identity.

Clary and Simon's relationship evolves significantly throughout the film. Initially, Simon is portrayed as Clary's best friend, who harbors unrequited feelings for her. As Clary becomes embroiled in the Shadow World, Simon struggles with feelings of jealousy and helplessness. His transformation into a vampire later in the film marks a turning point, complicating their friendship and introducing new dynamics as Clary navigates her feelings for both Simon and Jace.

Runes are magical symbols that Shadowhunters use to enhance their abilities, heal injuries, and provide protection. Each rune has a specific purpose, and Clary learns about their significance as she becomes more involved in the Shadow World. The runes symbolize the connection between the Shadowhunters and their heritage, and Clary's ability to create new runes becomes a pivotal aspect of her character development and her unique role in the unfolding conflict.