In 1957, an enormous alien robot plunges from the sky and lands near Rockwell, Maine, with no recollection of its existence. Shortly after its crash, the Iron Giant roams the landscape, sparking the curiosity of a brave nine-year-old boy named Hogarth Hughes, who diligently traces the path of the destruction through the forest. Upon finding the robot tangled in power cables at a local electrical substation, Hogarth frees him, forging an unexpected friendship. They return to Hogarth's home, where the boy lives with his widowed mother, Annie.
Excited by their newfound bond, the Giant's antics escalate when he whimsically tries to eat the rails from nearby railroad tracks. Hearing a train approach, Hogarth warns the Giant to fix the tracks, but the effort takes too long—a moment that leads to a train crashing into the Giant's head. In a rush to protect him, Hogarth hides the damaged robot in their barn, where he discovers that the Giant possesses the ability to self-repair.
As night falls, Hogarth returns to the barn with a pile of comic books to entertain his mechanical friend. The Giant is particularly taken with the story of Superman, but becomes anxious upon reading about an evil robot. Hogarth reassures the Giant that he can choose who he wants to be, encouraging him to embrace his identity.
Meanwhile, U.S. government agent Kent Mansley uncovers signs of the Giant's existence and becomes increasingly paranoid about a potential alien threat. He begins surveilling Hogarth to gather more intelligence, even renting a room in Hogarth's house after discovering a BB gun left behind by the boy. As Mansley sounds alarms about an alien invasion, Hogarth does his best to keep the Giant's existence a secret.
In an effort to protect his friend, Hogarth introduces the Giant to the beatnik artist Dean McCoppin. When Mansley and Lieutenant General Guy Rogard come snooping around, Dean cleverly passes off the Giant as an artistic creation, evading suspicion. However, during a playful moment involving a toy gun, the Giant's defensive mechanisms activate, prompting Dean to intervene and protect Hogarth.
Their adventures take them into the town of Rockwell, where the Giant performs heroically by saving two boys, quickly earning the affection of the townsfolk. However, not all is well; the military, having caught sight of the Giant, moves in for an attack. When the Giant is struck and crashes to the ground, he mistakenly assumes that Hogarth has perished. This mistake leads to a vengeful outburst, where the Giant retaliates against the army, displaying overwhelming firepower.
Amidst confusion and deception, Mansley manipulates Rogard into believing that the Giant has harmed Hogarth, urging him to target the Giant with a nuclear missile from the USS Nautilus. Having awakened to the chaos, Hogarth rushes to calm the Giant down, fully aware of the impending disaster. He bravely confronts Rogard, revealing the truth and attempting to mitigate the situation.
As the conflict escalates, Mansley, fearing for his own safety, tries to flee while the Giant heroically decides to intercept the missile. With the resolute heart of a true hero, the Giant soars high into the sky, colliding with the missile and creating an awe-inspiring explosion that lights up the atmosphere—a final act of bravery that saves Rockwell but leaves the townspeople, particularly Hogarth, mourning the loss of their friend.
In the aftermath, Annie and Dean begin a relationship, with Dean crafting a statue in honor of the Giant's memory. Just when Hogarth thinks he’s lost the Giant forever, a package arrives from General Rogard containing a small piece of the Giant—an invaluable jaw bolt. That night, a familiar beeping awakens Hogarth; realizing the Giant may still be alive and repairing itself, he opens the window, allowing the bolt to escape. Far away on the Langjökull glacier in Iceland, the various parts of the Giant draw closer to where his head lies, eyes glowing with newfound life, as the Iron Giant awakens, ready for new adventures.
