"DNA²" is a science fiction romantic comedy anime set in a future where overpopulation has become a critical issue. To combat this, scientists develop a method to genetically modify individuals to reduce their reproductive instincts. However, a genetic anomaly known as the "Mega-Playboy Syndrome" emerges, causing certain individuals to exhibit uncontrollable hyper-sexual behavior. The story centers on Junta Momonari, a high school student with a peculiar condition: he becomes nauseous and faints at the sight of attractive women. This condition stems from his latent Mega-Playboy genes, which have not yet fully activated.

The narrative takes a dramatic turn when Karin Aoi, a time-traveling agent from the future, arrives to prevent Junta from triggering his Mega-Playboy Syndrome. Her mission is to alter his genetic code to ensure he does not father 100 children in the future, which would exacerbate the overpopulation crisis. Karin attempts to use a special DNA-altering dart gun to neutralize Junta's genes, but her efforts are complicated by his unpredictable reactions and the interference of other characters.

As the story progresses, Junta's latent powers begin to manifest, leading to chaotic and often humorous situations. His interactions with Karin and other female characters, such as his childhood friend Ami Kurimoto, create a dynamic mix of romantic tension and comedic misunderstandings. Ami harbors feelings for Junta, but his condition and Karin's presence complicate their relationship. Meanwhile, Ryuji Sugashita, a rival with his own Mega-Playboy abilities, adds further conflict as he competes for the affections of the same women.

The series explores themes of genetic destiny, free will, and the consequences of tampering with nature. Junta's struggle to control his emerging powers and Karin's determination to complete her mission drive the plot forward. The interplay between the characters' personal desires and the larger societal implications of their actions creates a layered narrative that balances humor, romance, and science fiction elements. The story culminates in a resolution that addresses both the immediate conflicts and the broader implications of the Mega-Playboy Syndrome, offering a satisfying conclusion to the series.