In “the not-too-distant future”, where liberal eugenics is common and DNA plays the primary role in determining social class, Vincent Freeman (Ethan Hawke) is conceived and born without the aid of this technology. His parents regret this, and his younger brother, Anton, is conceived with the aid of genetic engineering. Growing up, their father clearly favors Anton, the stronger, taller and more perfect son. Vincent dreams of a career in space, but his parents remind him that his imperfections will preclude from ever achieving this. Vincent and Anton enjoy playing a game that they called "chicken" – both would swim out into the sea, and the first person to tire out and swim back to shore would be the loser. As children, Anton always won due to his superior genes.

However, one day when they were older, Vincent threw caution to the wind and gave everything he got during this game – he overtook Anton, who cried out to his older brother for help as he was about to drown. Vincent saved Anton by pulling him to the shore. Vincent then left home shortly thereafter.

Suffering from the nearly eradicated physical dysfunction of myopia, as well as being given a life expectancy of 30.2 years (mostly because of a heart disorder probability of 99%), Vincent faces extreme genetic discrimination and prejudice. The only way he can achieve his life-long dream of becoming an astronaut is to break the law and impersonate a "valid", a person with appropriate genetic advantage.

He assumes the identity of Jerome Eugene Morrow (Jude Law), a former swimming star who, despite a genetic profile "second to none", won only a silver medal in a high-profile competition. He then attempted to commit suicide by jumping in front of a car, but again fell short of his goal in that he only succeeded in paralyzing himself from the waist down. However, as the incident occurred outside the country, no one knows of his newly acquired disability. Thus, Vincent can "buy" his identity with no one the wiser. Though he requires limb lengthening to increase his height, persistent practice to favor his right hand instead of his left, and contact lenses to replace his glasses while matching Jerome's eyes, he can use Jerome's "valid" DNA in blood, tissue and urine samples to pass any genetic test — as long as he takes extreme measures to leave no traces of his identity as an "in-valid".

But, where he was once an object of scorn and pity, he is now a perpetrator of an unspeakable fraud. Legally, exposure would only subject him to fines, but socially the consequences would be far more extreme — he is now a heretic against the new order of genetic determinism. Vincent is now a "borrowed ladder" (a play on words referring to both the structure of an un-coiled DNA strand and the idiom of altitude as social status) or in harsher language, a de-gene-erate.

With Jerome's impressive genetic profile he easily gains access to the Gattaca Aerospace Corporation (his interview consists entirely of a genetic analysis of a urine sample), the most prestigious space-flight conglomerate of the day. With his own equally impressive determination, he quickly becomes the company's ace celestial navigator. But a week before Vincent is scheduled to leave for Saturn's moon Titan, the mission director is murdered, and evidence of Vincent's own "in-valid" DNA is found in the building in the form of an eyelash. The presence of this unexpected DNA attracts the attention of the police, and Vincent must evade ever-increasing security as his mission launch date approaches and he pursues a relationship with his co-worker Irene Cassini (Uma Thurman).

After numerous close calls, the investigation eventually comes to a close as Director Josef (Gore Vidal) is arrested for the murder by the detective covering the investigation (Alan Arkin). The Director reveals that he murdered the mission director in order to buy time for the mission to launch, because the window of opportunity for the launch is only open once every seventy years, and that it is now too late to stop the launch. However, just as Vincent appears to be in the clear, he is confronted by the chief detective, who is revealed to be Vincent's estranged brother, Anton (Loren Dean).

Anton tries to convince Vincent to go with him for protection before Vincent is found out. However, it soon becomes apparent that Anton is acting more out of insecurity and is more concerned with how Vincent had managed to get the better of him, despite Anton's supposed genetic superiority. Vincent and Anton settle their competition as they did when they were children, by seeing who could swim out into the ocean farthest. As he did once before when they were young, Vincent manages to beat Anton who, once again, is rescued by his older brother. This is simply because Vincent refused to save any strength to swim back — he is willing to risk everything to succeed. Conversely Anton is worried about preserving enough strength to swim out and return again, and these fears kept him from testing his true limits.

As the day of the launch finally arrives, Jerome bids Vincent farewell and says that he intends to travel too. He reveals that he has stored enough genetic samples to last Vincent two lifetimes. Overwhelmed and grateful, Vincent thanks Jerome for "lending" him the identity that has allowed his success at Gattaca. Jerome replies, however, that it is he who should be grateful, since Vincent lent Jerome his dreams. As Vincent moves through the Gattaca complex to the launch site, he is stopped for an unexpected urine test. Vincent reluctantly agrees to take the test, even though he has not brought any of Jerome's genetic material to hide his identity.

The test result uncovers Vincent's "in-valid" status, and the doctor, Lamar, reveals that he has known Vincent's true identity all along, saying: "For future reference, right-handed men don't hold it with their left. Just one of those things". Lamar then alters the test result to allow him to proceed regardless, confessing that his son admires Vincent, and wants to be an astronaut just like him, despite an unforeseen genetic defect that would already rule him out. As the shuttle lifts off, Jerome is shown committing suicide inside his home incinerator, wearing his silver medal, which turns gold in the flames.

The story centers on the irony of the perfect Jerome failing to succeed despite being given every advantage while the imperfect Vincent transcends his deficiencies through force of will and spirit. A milder version of the disorder that afflicts Vincent prevents Irene from taking part in space flight. This dichotomy shows how the eugenic policy in Gattaca and the world in which it is set adversely affect the humanity of both Vincent and Jerome, as well as the "invalid" and "valid" humans they represent.

A coda, cut from the final film, lists various people who have succeeded despite genetic deficiencies (and would be excluded in the modern society of Gattaca), such as Albert Einstein, Abraham Lincoln, and John F. Kennedy.

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