In the year 2011, a catastrophic pathogenic virus wiped out a staggering 99 percent of the global population, which forced the remaining survivors to scatter across the devastated Earth. Amid this chaos, a scientist named Trevor Goodchild developed a potential cure to the deadly virus. Fast forward to 2415, the Earth has transformed dramatically, with a mere five million humans now residing in Bregna, a walled city-state that presents a façade of utopia yet is fraught with darkness.
Bregna is governed by a council of scientists, including the ruling Goodchild dynasty that has held power for 400 years. However, this seemingly idyllic society has a sinister undertone, as citizens often disappear, haunted by nightmares that plague the populace. Although the regime promises to provide for the city, it demands that individuals surrender their freedom, forcing them into a life of quiet resignation within their “gilded cage.” High above the city looms the Relical, a dirigible symbolizing the grim history the citizens cannot forget. The city's borders are sealed by an impregnable wall, keeping them from the world beyond.
Enter Aeon Flux (Charlize Theron), a fierce warrior and member of the underground resistance known as the Monicans, who utilize telepathy-enhancing technology to coordinate their efforts. Under the leadership of the Handler, Aeon sets forth on a mission to disrupt the authoritarian regime. After her attempt to destroy a surveillance post, she returns home to discover that her sister Una (Amelia Warner) has been tragically mistaken for a Monican and killed. Devastated, Aeon feels as though her life has been irrevocably taken from her, intensifying her resolve to dismantle the Goodchild power structure.
Charged with the task of assassinating the government's key figure, Trevor Goodchild, Aeon must navigate the treacherous citadel where he addresses the scientist congress. To reach him, she crosses the Frontier Garden, a realm heavily fortified with lethal defenses, including self-targeting darts and concealed razor blades. As she reaches the Forum, Trevor grapples with the brutal tactics employed by his brother Oren against the Monicans, worrying that mere force will not suffice in quelling the uprising. Despite knowing the oppressive system they’ve built must evolve, Oren remains convinced it can be maintained.
In a twist of fate, as Aeon aims to kill Trevor, she is struck by memories that emerge — tender flashbacks of a kiss and the name "Katherine" rolling off Trevor's tongue. This moment of hesitation leads to her capture, unveiling a nefarious plot orchestrated by Oren who had secretly informed the Monicans of her mission. However, Aeon manages to escape, discovering Claudius (Nikolai Kinski), her sister's husband, alive in the citadel. He reveals Trevor's good intentions—his research aims to resolve the nightmares and disquieting memories plaguing the citizens.
Aeon's path continues to intertwine with Trevor's as they grow closer, eventually culminating in a moment of intimacy amidst the danger. Yet, she is soon forced to flee when Oren’s guards attack her within Trevor's secret laboratory. Angry over Aeon’s failure to eliminate Trevor, Sithandra (Sophie Okonedo) refuses to help her probe deeper into Trevor’s true intentions.
Determined to uncover the truth, Aeon infiltrates the Relical and confronts Keeper (Pete Postlethwaite), the enigmatic overseer. Heart-wrenchingly, she discovers that Una was "recycled," given a new identity. Meanwhile, Oren's ruthless ambitions come to a head as he publicly brands Trevor a traitor.
Aeon embarks on a painful journey to uncover the secrets of Bregna’s origins, culminating in Trevor unveiling that the inhabitants are, in fact, clones cultivated from recycled genetic material. With the original humans rendered infertile by the antidote to the virus, the cycle of death and rebirth prevailed, resulting in troubling dreams and eerie memories of past lives.
Trevor’s creations, including Una—an evidently successful clone—hold secrets that galvanize Oren's fear and push him to terminate all those who threaten his reign. With the truth laid bare, Aeon finds herself not only at odds with Oren but also with the Monicans who once fought alongside her and aim to eliminate Trevor.
In a climactic turn, Aeon rallies her allies, including Sithandra, to take down Oren and his loyalists, aiming for the Relical as her target. Inside, she discovers the remnants of her heritage, along with the shocking preservation of Katherine's DNA. In a monumental resolution, the dirigible crashes into the city’s wall, unveiling the untamed world beyond their confines for the first time in centuries. The journey culminates in an awakening for both Aeon and the people of Bregna, now faced with the reality of their existence and a glimmer of hope for genuine freedom.
