Richard Phillips takes command of MV Maersk Alabama, an unarmed container vessel from the Port of Salalah in Oman, with orders to sail through the Guardafui Channel to Mombasa, Kenya. Wary of pirate activity off the coast of the Horn of Africa, he and First Officer Shane Murphy order strict security precautions on the vessel and carry out a practice drill. During the drill, the captain notices that the vessel is being followed by Somali pirates in two skiffs, and calls for help. Knowing that the pirates are listening to radio traffic, he pretends to call a warship, requesting immediate air support. One skiff turns around in response, and the other – crewed by four armed pirates led by Abduwali Muse – loses engine power trying to steer through Maersk Alabama‘s wake.

The next day, Muse’s skiff, now fitted with two outboard engines, returns with the same four pirates aboard. Despite the efforts of Phillips and his crew, the pirates secure their ladder to the ship. As they board, Phillips tells the crew to hide in the engine room, just before the pirates storm the bridge and hold Phillips and the other crew members at gunpoint. Phillips offers Muse the $30,000 in the ship’s safe, but Muse’s orders are to ransom the ship and crew in exchange for millions of dollars of insurance money from the shipping company. While they search the ship, Shane sees that the youngest pirate Bilal does not have sandals and tells the crew to line the engine room hallway with broken glass.

Chief Engineer Mike Perry deactivates the power to the ship, plunging the lower decks into darkness. Bilal cuts his feet when they reach the engine room, and Muse continues to search alone. The crew members ambush Muse, holding him at knifepoint, and arrange to release him and the other pirates into a lifeboat. However, Muse’s right-hand man Nour Najee refuses to board the lifeboat with Muse unless Phillips goes with them. Once all are on the lifeboat, Najee attacks Phillips, forcing him into the vessel before launching the boat with all five of them on board.

As the lifeboat heads for Somalia, tensions flare between the pirates as they run low on the plant-based amphetamine khat that they have been chewing, and they lose contact with their mother ship. Najee becomes agitated and begins to question Muse’s leadership when they are intercepted by the U.S. Navy destroyer USS Bainbridge. Bainbridge‘s captain Frank Castellano is ordered to prevent the pirates from reaching the Somali coast by any means. Even when additional ships arrive, Muse asserts that he has come too far and will not surrender. The negotiators are unable to change his mind, and a team from DEVGRU parachutes in to intervene, while Phillips attempts to escape from the lifeboat before being quickly recaptured and repeatedly beaten by Najee.

While three DEVGRU marksmen get into positions, Castellano and DEVGRU continue to try to find a peaceful solution, eventually taking the lifeboat under tow. Muse agrees to board Bainbridge, where he is told that his clan elders are arriving to negotiate Phillips’s ransom. In the lifeboat, Phillips prepares a goodbye letter to his wife in case he is killed, while Najee decides to take full control. Najee spots Phillips writing the letter and snatches it. Phillips attacks Najee until Bilal subdues him by striking him in the back with his gun.

The pirates tie up and blindfold Phillips, and Najee beats him further. As Najee prepares to shoot Phillips, Bainbridge‘s crew stops the tow, causing Elmi, Bilal, and Najee to lose balance. This gives the marksmen three clear shots, with which they simultaneously kill all three pirates. Muse is arrested and taken into custody for piracy. Phillips is rescued from the lifeboat and his injuries are treated. Although in shock and tears, he thanks the rescue team for saving his life.