In a mysterious mausoleum filled with cats in Central City, Denny Colt (Gabriel Macht), also known as the masked vigilante The Spirit, receives an urgent phone call from Detective Sussman (Dan Gerrity). A major disturbance has been reported near an old shipwreck in the mudflats, potentially linked to his arch-nemesis, The Octopus (Samuel L. Jackson). As The Spirit dons his heroic attire, he reflects on his deep love for the city while leaping across rooftops. In an alley below, he intervenes in a mugging, sustaining a knife wound without even flinching. The victim, bewildered, asks, "What are you?" but The Spirit dashes away, catching a lift with Officer Liebowitz (Frank Miller) toward the mudflats.
At the swamp, a captivating femme fatale, Sand Saref (Eva Mendes), emerges, seemingly gunning down Sussman. Though The Spirit and Liebowitz discover Sussman bleeding, a memory reveals it was the Octopus who fired the shots while searching for two identical chests submerged underwater. Sand, alongside her husband Mahmoud (Eric Balfour), attempts to escape with the treasure but ends up leaving one chest behind as the Octopus retrieves it.
Following the gruesome demise of Liebowitz, who is killed in a particularly brutal fashion, the Octopus dispatches his cloned henchmen—Ethos, Pathos, and Logos (all played by Louis Lombardi)—to confront The Spirit. Meanwhile, Silken Floss (Scarlett Johansson), who works for the Octopus, arrives in an unsettling manner, accidentally running over one of the clones. She expresses her certainty that the night will see a continued battle between the two formidable foes.
A dramatic showdown ensues as The Spirit and the Octopus engage in a highly stylized fight. Despite being resilient, The Spirit is momentarily incapacitated when Pathos shoots him. As luck would have it, The Spirit is revived by his lover Dr. Ellen Dolan (Sarah Paulson), the daughter of Police Commissioner Dolan. Despite his injuries appearing miraculously healed, Commissioner Dolan scolds The Spirit for recklessly endangering his officers while pursuing the Octopus without authorization.
In a hidden lair, the Octopus and Silken Floss uncover that their chest does not contain the sought-after Blood of Heracles but rather an enigmatic glowing object. Infuriated, the Octopus takes violent measures against his clones when he learns of Sand's involvement, indicating that he plans to orchestrate a swap.
Meanwhile, Sand and Mahmoud visit a fence named Donenfeld (Richard Portnow) to seek the location of the treasure. Subsequently, Sand makes a drastic move by transferring Donenfeld's payment to another account and coercing him to end his life. The Spirit, reborn and healed, visits Ellen but faces a brief moment of temptation, which she skillfully navigates due to her understanding of The Spirit's nature.
A critical piece of Sand's past unfolds—her history as a renowned jewel thief and how her childhood friendship with Denny Colt melded with their tragic backgrounds. When The Spirit confronts Sand, caught off-guard by her nudity, a fierce exchange occurs, leading to a shocking window dive, saving him from certain harm.
Eventually, The Spirit follows a lead that connects Pathos to the feiffer industrial salt plant, revealing the Octopus's hideout. While battling clones underground, The Spirit unexpectedly encounters Floss, who distracts him with a kiss before injecting him. When he regains consciousness, he finds himself in a bizarre setting surrounded by Nazi symbols and a performance by the enigmatic assassin Plaster of Paris (Paz Vega).
The Octopus's motive for immortality unfolds—a serum he created him using the Spirit's body for experimentation. As he intends to consume the mystical blood to elevate his power, Plaster unexpectedly aids The Spirit. With The Spirit regaining his strength, an explosive confrontation ensues, signaling the climax of their rivalry.
Wounded but determined, The Spirit plunges into the city docks, encountering the Angel of Death, Lorelei (Jaime King). He struggles between her haunting allure of acceptance and his responsibilities to the living—Ellen, Sand, and the city calling for him. After emerging from his watery retreat, The Spirit faces a final confrontation with the Octopus, leading to a bloody and chaotic conclusion.
In the end, The Spirit hands Sand her locket, rekindling their emotional connection amid Ellen's heartbreak. As old loves part, The Spirit seeks to mend his bond with Ellen, recognizing the fractures that define their relationship. In a twist of fate, Silken Floss discovers an ominous remnant of the Octopus, leaving the door open for future duplicity and villainy.
