"DNA²" is a science fiction anime series set in a future where overpopulation has become a critical issue. To combat this, scientists have developed a method to genetically modify individuals to reduce their reproductive instincts. However, a small percentage of people, known as "Mega-Playboys," possess a rare genetic mutation that causes them to have an uncontrollable urge to seduce women, leading to unintended pregnancies. The story centers on Junta Momonari, a high school student with a peculiar condition: he becomes violently ill at the thought of romantic or sexual situations, making him the opposite of a Mega-Playboy.

Junta's life takes a dramatic turn when Ami Kurimoto, a time-traveling agent from the future, arrives with a mission to neutralize him. Ami mistakenly believes Junta will become a Mega-Playboy in the future, responsible for fathering 100 children and exacerbating the overpopulation crisis. To prevent this, she attempts to inject him with a DNA-altering drug. However, the injection malfunctions, and Junta begins to transform into a Mega-Playboy whenever he experiences strong emotions. This transformation drastically alters his personality, turning him into a charismatic and flirtatious individual, much to the confusion of those around him.

As Junta struggles to control his newfound abilities, he becomes entangled in a love triangle involving Ami and his childhood friend, Maho Suzuku. Ami, despite her initial mission, begins to develop feelings for Junta, while Maho harbors her own unspoken affection for him. The series explores the complications arising from Junta's dual identity, his relationships with the two women, and the broader implications of his potential future as a Mega-Playboy.

Throughout the series, Ami works to correct her mistake and prevent the future she was sent to avert. The narrative delves into themes of destiny, free will, and the ethical dilemmas surrounding genetic manipulation. Supporting characters, such as Ryuji Sugashita, Junta's best friend, and Kotomi Ryuzaki, a fellow student with her own secrets, add depth to the story. The series balances comedic moments with dramatic tension, culminating in a resolution that addresses the consequences of Junta's actions and the choices made by the characters.