In 2005, NASA discovers an extrasolar planet with conditions similar to Earth. On the chance that it contains intelligent life, NASA transmits a powerful signal from a communications array in Hawaii, which will be boosted by a satellite in orbit. Around the same time, the talented but undisciplined slacker Alex Hopper (Taylor Kitsch) attempts to impress a woman by getting her a chicken burrito, the result of which sees him arrested for breaking into a convenience store. The woman is Samantha Shane (Brooklyn Decker), daughter of United States Pacific Fleetcommander Admiral Terrance Shane (Liam Neeson), who in turn is the superior of Commander Stone Hopper (Alexander Skarsgard), Alex’s older brother. Fed up and infuriated at Alex for lack of motivation and possibly ruining his own career, Stone forces him to join the United States Navy.
By 2012, Alex is a lieutenant and the Tactical Action Officer aboard the Arleigh Burke class destroyer USS John Paul Jones, while Stone is the commanding officer of USS Sampson. Alex is also in a relationship with Samantha and wants to marry her, but is afraid to ask her father for permission. During the opening ceremony for the RIMPAC naval exercises, Alex brawls with Japanese officer Captain Nagata (Tadanobu Asano), the latest in a string of incidents that could result in his discharge and the end of of his career. Meanwhile, Samantha, a physical therapist, accompanies retired Army veteran and amputee Mick Canales (Gregory D. Gadson) on a hike on Oahu to help him adapt to his prosthetic legs.
Five alien ships arrive in response to the NASA signal. One ship collides with an orbital satellite and crashes in Hong Kong, while four others land in the water near Hawaii. Sampson, John Paul Jones, and the JMSDF Kongo class destroyer Myōkō investigate, but are trapped when one of the ships erects an impenetrable force field around the Hawaiian islands. The destroyers attempt to establish contact, but the aliens attack in response to a warning shot fired by the American destroyers: Sampson and Myōkō are destroyed. John Paul Jones is damaged with the commanding and executive officers killed. Initially attached to Sampson, Alex, who was one of the few out to take a closer look at the alien vessels, now boards John Paul Jones and takes command as the most senior officer left on the ship. Although initially wanting to attack the aliens in retaliation for his brother’s death aboard Sampson, Alex is persuaded by other crew members to instead recover survivors from Myōkō, with Captain Nagata among them. This act prompts the aliens to call off another attack. Since the barrier prevents the use of radar and sonar, Nagata discloses that the Japaneses Navy uses the tsunami warning buoys around Hawaii to track the US Navy during previous RIMPAC exercises, subsequently the alien vessels’ movements can be tracked in a similar method.