"Weiß Kreuz" centers around four young men who operate a flower shop by day and function as covert assassins by night. The group, known as Weiß, consists of Aya Fujimiya, the stoic and disciplined leader; Ken Hidaka, the energetic and impulsive member; Youji Kudou, the charming and flirtatious individual; and Omi Tsukiyono, the youngest and most tech-savvy member. Each member has a personal vendetta or tragic past that drives their involvement in the group, and their missions often target corrupt individuals who exploit the vulnerable.

The narrative unfolds as Weiß carries out assignments under the direction of a mysterious figure known only as "Persia," who provides them with targets and resources. Their missions frequently intersect with a rival group called Schwarz, composed of four equally skilled assassins: Schuldig, a telepath with a sadistic streak; Crawford, a precognitive strategist; Nagi, a telekinetic with a calm demeanor; and Farfarello, a fanatical and self-destructive fighter. The rivalry between Weiß and Schwarz is marked by ideological differences, with Weiß seeking justice for the oppressed and Schwarz embracing chaos and destruction.

As the series progresses, the personal histories of the Weiß members are gradually revealed. Aya’s motivation stems from the abduction of his younger sister, Aya-chan, who was subjected to cruel experiments by a shadowy organization. Ken seeks vengeance for the murder of his girlfriend, while Youji grapples with the trauma of his mother’s death and his father’s criminal activities. Omi, initially portrayed as the most innocent, harbors a dark connection to the organization that manipulated his past. These backstories add depth to their characters and provide context for their actions.

The plot intensifies as Weiß uncovers the extent of the organization’s influence, which ties directly to their personal grievances. The group’s missions become increasingly perilous, culminating in confrontations with Schwarz and the revelation of Persia’s true identity. The series explores themes of justice, revenge, and the moral ambiguity of their actions, as the members of Weiß struggle to reconcile their ideals with the violence they perpetrate.

The dynamic between Weiß and Schwarz serves as a central narrative thread, with their encounters highlighting the contrast between their methods and philosophies. The series balances action-packed sequences with moments of introspection, delving into the psychological toll of their double lives. The interplay between the characters’ personal struggles and their collective mission drives the story forward, creating a compelling blend of action, drama, and mystery.