As the war-torn skies of 1943 Tokyo reverberate with the distressing sound of sirens, a desperate Mahito Maki emerges from his home, racing toward the inferno consuming the hospital where his mother, Hisako, is trapped. His anguished cries of “Mother!” pierce the desolate streets as panic twists his features.
In the aftermath of Hisako's tragic loss, a grief-stricken Mahito begins a new chapter in life alongside his father, Shoichi Maki, at their countryside arsenal, where they attempt to rebuild amidst the chaos of wartime. It is here that Shoichi wedlocks with Natsuko, who harbors a secret of her own: she is with child.
Settling into Natsuko's sprawling estate, Mahito finds himself surrounded by seven enigmatic maids, drawing his attention to the elusive Grey Heron that flutters about the grounds. His intrigue leads him to a mysterious tower constructed by Natsuko's grandfather before her birth, which conceals secrets and hidden mysteries.
As the cruel realities of war unfold, Mahito encounters bullying at school, driving him into a desperate state. He resorts to self-harm to assert his strength but is rescued from his anguish by his father. During his recovery, he discovers a treasured book from his mother titled "How Do You Live?"—a poignant reminder of her love and wisdom that now comforts him.
Yet, the shadows of Hisako's fiery demise linger, haunting Mahito with vivid nightmares. It is in this tumultuous time that he again meets the mystical Grey Heron, which taunts him with cryptic messages and invites him into a mysterious realm. Following its call, Mahito finds himself amidst an eerie assembly of frogs, which serves as a forewarning of more trials ahead.
Sensing the looming specter of doom, the estate's maids scramble toward the tower, leaving behind an unsettling atmosphere. In horror, Mahito witnesses Natsuko vanish into the depths of the mysterious structure, urging him to pursue her. As Mahito's journey continues, a curious maid joins his quest towards the tower, led by the Heron's ethereal guidance, only to uncover unsettling illusions—a vision of Hisako, who materializes only to dissipate at Mahito's touch.
Frustrated and confused, Mahito scolds the Heron, which then conjures a diminutive, bald figure. In a bizarre turn, the Heron's beak, pierced by an arrow made of its own feather, transforms it into a short, pudgy man, drawing Mahito and the maid into the floor below, where they navigate a mystical world.
Suddenly, Mahito finds himself on an unfamiliar island, threatened by a ravenous flock of pelicans. Thankfully, Kiriko, a resourceful sailor, rescues him from the attacking birds while chastising him for his reckless actions. As they journey back to her home, Kiriko shares chilling tales of phantoms that haunt her mystical world.
Once at her abode, Kiriko looks after the Warawara—tiny, marshmallow-like spirits dependent on her nourishment to transcend into the spirit world. As they prepare a feast together, Mahito begins unraveling the truth about Kiriko’s identity, realizing she is none other than the maid that accompanied him into the spirit realm, surrounded by figurines of the other elderly maids from her past.
When night descends, Mahito and Kiriko witness the ascension of the Warawara, interrupted by a sudden attack from more pelicans. Amid the chaos, Lady Himi, a girl with fiery abilities, appears just in time. Mahito's next encounter is with the lead Noble Pelican, Willem Dafoe, whose dying whisper reveals that the pelicans' actions against the Warawara were borne out of sheer desperation.
Still battling his inner turmoil, Mahito shares a meal with the Heron for what may be the last time, as Himi’s assistance becomes crucial in repairing the Heron's beak, freeing it from its natural constraints. However, their reunion proves fleeting, as Mahito soon finds himself amidst gigantic parakeets claiming to lead him to Natsuko—though their true motives are far from innocent. Fortunately, Himi intervenes, utilizing her fiery powers to scatter the aggressive creatures and reveal their deception.
Enlightened by Himi, Mahito learns she is Natsuko’s sister and that the Tower Master—the figure entwined with the celestial mysteries—created this realm along with its portals. Himi is determined to help Mahito reach a portal that could return him to his world. Yet, as they move forward, they are relentlessly pursued by the parakeets, and Mahito’s father, along with the maids, frantically search for both him and Natsuko.
Resolute not to abandon his quest, Mahito chooses to remain in the mystical realm to reunite with Natsuko. However, he ultimately succumbs to unconsciousness. During his slumber, a maid divulges the tower’s haunted history, establishing it was crafted from a meteorite—an event preceding Hisako's unexplained disappearance a year before her return.
Mahito is summoned by the enigmatic Granduncle, who perceives potential in him as a successor. The elder seeks to draw upon Mahito's lineage and pure intentions to liberate this world from its encumbering horrors. Mahito acknowledges his scar, a physical testament to the darkness he confronts.
Upon awakening, Mahito finds himself ensnared by the parakeets once more. The vigilant Heron infiltrates their territory, dispatching foes to rescue Mahito. Together, they converge at the chamber where Natsuko is imprisoned. However, when Mahito attempts to liberate her, a mystical energy encircles them, rendering her cold and indifferent towards him. His declaration that she will be his mother ignites a flicker of recognition that allows her animosity to fade and her true self to resurface.
As Mahito and the Heron embark on a bold mission to rescue Himi from the clutches of the Parakeet King (Dave Bautista), they stumble into a convoluted plot. The Parakeet King, in covert partnership with Granduncle, works to maintain dominion over his forces and the precarious balance of this whimsical world. Once liberated, Mahito is faced with a heart-wrenching decision: to continue under Granduncle's guidance or carve his path, preserving the friendships nurtured amidst turmoil. Enraged by Mahito's reluctance to submit, the Parakeet King topples Granduncle's towering creation, sending shockwaves that threaten to fracture reality itself.
As the world spirals into chaos, Granduncle disappears, delivering a heartfelt farewell to his descendants. Himi bids Mahito and Natsuko goodbye, unveiling her identity as a younger Hisako—a twist that significantly alters the trajectory of their lives.
In the wake of the world-ending catastrophe, Mahito and his companions embark on a desperate flight through the collapsing landscape, narrowly escaping as reality crumbles. In the aftermath, Mahito reunites with Shoichi and Natsuko, alongside Kiriko, who, bearing the wisdom of their shared past, shows Mahito the importance of their connection. The Heron, in its unwavering guidance, imparts its final words of wisdom, reminding Mahito that eventually, he may forget the world they leave behind—a poignant reflection on the profound bonds created through their adventures.
Two years later, Mahito returns to a transformed Tokyo with Shoichi, Natsuko, and his younger brother—his journey now a tangible testament to the enduring strength of friendship and the resilience of the human spirit in the face of overwhelming adversity.
