Helen Benson (JENNIFER CONNELLY) is a professor of astrobiology at Princeton who's raising her young stepson, Jacob (JADEN SMITH), following the death of the boy's military father in the past year. Due to her credentials, but out of the blue, she's contacted and immediately picked up by the Feds and whisked away to New York City along with various other scientists and specialists. It seems a deep-space object is hurtling toward Earth and specifically Manhattan, but as everyone braces for the impact, the object slows and then lands in Central Park.
As Helen goes to meet the visitor who disembarks from the enormous sphere of a spaceship, someone in the military opens fire, downing the extraterrestrial. As a result, an enormous robot (later given the acronym G.O.R.T.) comes out and disarms the hostile forces, thus allowing Helen, her government friend Michael Granier (JON HAMM), and others to whisk the alien away for immediate medical care. And what's found under an epidermis that sloughs off is Klaatu (KEANU REEVES), the alien in human form, who quickly heals and regains both his strength and consciousness.
While the scientists are fascinated, Secretary of Defense Regina Jackson (KATHY BATES) is worried, not only because Klaatu's ship managed to avoid American military defenses, but also because he seems to have accessed most all data regarding the government and its people. Despite him wanting to address the United Nations, she's more intent on interrogating what she views as a national threat. He manages to escape, however, and having previously assessed that Helen is the only benevolent human he's encountered, he contacts her for help.
After learning that he's there to save the planet by ridding Earth of all humankind for their ecologically destructive ways, Helen, with Jacob in tow, tries to change his mind, including by taking him to visit the brilliant Professor Barnhardt (JOHN CLEESE). Yet, Regina and the rest of the government are still after him (while also attempting to dissect the impenetrable GORT), thus forcing Helen, Jacob and Klaatu to go on the run, all as she tries to convince Klaatu, before it's too late, that humans deserve a second chance.