In 1962, President Kennedy, believing that the wars of the future would be low intensity conflicts such as guerilla wars and acts of terrorism, created an elite special forces unit to meet the enemy on his own turf. Experts in sea-air-land operations, they are known as NAVY SEALS.
The USS Forrestal, an aircraft carrier, is on station in the Eastern Mediterranean Sea in modern times. On the bridge, the watch receives a May Day from a cargo ship somewhere else in the Mediterranean. The ship reports that they have been attacked, are on fire and adrift. Wounded men scramble to flee the burning ship. A Navy Sea King helicopter approaches, asking the Forrestal's watch commander for permission to land to remove the trapped sailors from the burning ship.
As the helicopter prepares to set down on the port side of the ship, a gunboat speeds around the starboard, aiming heavy guns at the unarmed chopper. The helicopter is under attack, receiving fire from the gunboat, sustaining casualties and wounded, as their chopper loses its rotor.
As the scene shifts, a dark headed man wakes, laying in the early morning surf on a beach in Norfolk, Virginia. He has obviously enjoyed a night of revelry, but now he staggers toward houses along the beach, hung over and miserable. His name is Hawkins. He is met by another blond-headed, green eyed man, also hung over, coming out of one of the houses. The second man is looking for a third person named Graham. It becomes obvious that the revelry has been a bachelor party, and the three men are friends: Hawkins, James Curran, and Graham. The men dress and leave quickly in a jeep with James driving, heading for the wedding of the somewhat reluctant groom, Chief Graham. Only two of the three arrive at the wedding. Hawkins bails out, literally, by diving from the jeep into the harbor.
The wedding never happens. In the middle of the processional of the bride, beepers begin to sound throughout the church, and a large group of men, including the groom and best man, instantly leave, the bride left standing in the aisle. The men are a team of Navy SEALs. The beepers are their call to duty. With no hesitance, they leave family and friends behind and answer the call to go on an as yet unknown mission, with Curran now identified as the leader of the Team.
Cut to a Seaport in the Eastern Mediterranean, where a truck carrying a tall Middle Eastern man, obviously a person in command, to a building where a truck is being loaded. The terrorist leader chastises one of his crew for shooting down a helicopter. As he enters an upper room in the building, he sees a group of men, all tied to chairs, being guarded by his terrorist. The leader gives an immediate order to kill the prisoners, who are the crew from the Sea King helicopter previously shot down in the Mediterranean.
One prisoner is executed on the spot, and the Middle Eastern terrorist, begin to savagely beat the others. As the helicopter pilot is threatened at gunpoint, doors and windows on the upper floor of the building, and a skylight from above, all suddenly filled with black clad forms who barge their way in using silenced weapons, kill the guarding terrorist and rescue the remaining prisoners from certain death. There are seven of the rescuers in total, and Curran, Hawkins, and Graham lead the charge. There are other men who were also at the wedding in Norfolk, all part of this team of Navy SEALs.
The Middle Eastern leader, hiding in an adjoining room, is detected by Hawkins, but manages to evade capture by claiming to be an Egyptian sailor also being held by the terrorist in the building. In entering the room where the Leader is hiding, Hawkins breaks military silence, and alerts other Middle Eastern terrorist of the Team's presence in the building. Pressed for time to reach their extraction point, the SEAL Team battles their way through the streets of the seaport. Reaching their lift zone proves to be more challenging and deadly than the Team had expected, but as they move toward the dock area, a hidden member of the Team appears to give much needed back up. Hawkins and Graham, who had stayed behind to provide cover for the fleeing Team, stumble upon crates of large munitions. Rejoining the rest of their Team, the two men inform their commanding officer, Curran, of the presence of the missiles. The lieutenant chooses to extract his Team and the injured helicopter crew, leaving the missiles behind. The Team is lifted to safety by a Navy helicopter. During the escape, one SEAL is seriously wounded, but the Team and the rescued chopper crew are extracted to safety.
Onboard a aircraft carrier later that night, the Team members are interrogated by a group from Naval Intelligence, who question their every move and the lieutenant's decision to leave the Stinger missiles behind. It is apparent that there is no easy cooperation between the Intelligence agents and the SEAL operatives. It is also obvious that Hawkins is highly agitated by the mission and has trouble dealing with the emotional upheaval the 'deed' provides. The lieutenant tries to calm him down, but his advice receives marginal reception from the junior grade lieutenant.
On another day, in Washington, D.C., the Middle Eastern leader, identified as Ben Shaheed, is seen in an interview with a dark headed woman. At the Pentagon, either simultaneously or quickly thereafter, a group of military and civilian men watch the interview on screen. The interviewer is identified as Claire Verrons, a journalist and author, who is half Lebanese. Her questioning of Shaheed identifies that he and his group participated in the bombing of the Marine barracks in Lebanon in 1983. The Leader admits the complicity freely, saying they only sought revenge for the bombing of their homes by Navy ships and warplanes.
The man in charge of the meeting, seemingly the Secretary of State, pulls as much information about the journalist and the terrorist leader as he can from the people in the room. The Leader is part of a new terrorist organization in Lebanon known as Al Shudadah. On the opposite side of the table from the civilian and military interrogators sit a Naval Admiral, a Captain, and the SEAL lieutenant who decided to leave the missiles behind. The lieutenant is obviously heartsick over what the group of people label as a failure on the part of his Team. The Secretary of State takes opportunity to denigrate the man, noting that SEALs are expected to die if necessary to see that a mission is carried out. The meeting ends with the lieutenant asking for a chance to take his Team back in to destroy the missiles.
Following the meeting, leading his lieutenant across the open area of the harbor, the Captain tries to encourage the younger officer, whose name is finally identified as James Curran. Curran wants the chance to retry the mission, having taken to heart the Secretary's comment about SEALs being willing to die to get things done. The Captain expresses feelings that Curran's team would most likely have died had they tried to capture the ordinance, and they still would not have gotten to the missiles. The Captain orders the Team to stand down and get perspective on what happened during their last mission. A reluctant Curran agrees to the order.
Leave time for the SEALs includes a day of golfing... SEAL style, which means they don't exactly follow any of the rules. The Team is all together. Even during this "down time," Curran prepares for the "deed" to come; the Team's chance to find the missing Stinger missiles. He spends part of his day reading the book Tears of Rage: Inside the Mind of a Terrorist by Claire Verrons. Hawkins is surprised that Curran is still fixated on the possibility of the mission, reminding him that SEALs have to keep emotions under control.
During the golf outing, Graham convinces his fianceé to try to finish the wedding again. They agree again to marry. At the same time, the daredevil junior lieutenant, Hawkins, finds his car being towed from the fairway of the golf course. Always the crazy one, he steals a bicycle, chases the tow truck, and in the middle of heavy traffic, retakes his car from the truck's bed.
The Team receives their orders for a mission. Intelligence has heard that the Stinger missiles are onboard a merchant ship, The Latanya, off the coast of Syria. The Team is assigned to deploy from a submerged submarine, The Nyack, to board the ship, avoid the Muslim pilgrims on the ship, and locate the missiles. They face another serious danger as the missiles might be booby-trapped.
Through the dark, the SEALs maneuver to board the ship stealthily. They are quick and quiet, until Hawkins and another SEAL named Leary are forced to kill a terrorist who is holding one of the pilgrims hostage. Another terrorist, in the hold with what appears to be missile crates, falls on his own grenade. When the SEALs have the ship contained, a bomb squad brought in to check the crates, informs Curran and Hawkins that the "missiles" are just a decoy. The Team has lost again.
Back in the United States, Curran determines the only hope for the SEALs to complete this mission is to get better intelligence than the Intelligence Agencies are providing. He determines that his only hope is to talk with Claire Verrons and solicit her cooperation. He visits her at her studio. She is instantly wary of why a SEAL is coming to her for information. She requests a tour of the SEAL base, and Curran provides more of a tour than she expects. She is fine when he takes her to visit training facilities, but isn't quite prepared for the very real tour he gives her of the Kill House, a building used to train SEALs for close quarter battle. She leaves, but Curran follows, trying to convince him that he needs her help.
Curran attempts to woo the journalist over an elegant dinner. However, Hawkins has designs of his own on the woman, and has Curran paged in order to take over Curran's supposed 'date' with Claire. Curran suspects Hawkins is up to something, but he has no choice but to answer the page. He leaves Claire with Hawkins set to provide a ride home.
Hawkins proves to be a cad, insulting the woman's ancestors by referring to all Lebanese as "Rags" and using equally offensive epithets for all nationalities. As he drives her to her hotel, the man clumsily tries to seduce Claire, but she orders him to take her to her place. Meanwhile, Curran has discovered Hawkins' ploy and returns to confront the man. In their conversation, Curran reveals that since Intelligence agencies will give them no information, the Team has no one to turn to except Claire.
Within no time, the SEALs receive news that the Stingers have been used to shoot down a peace delegation in Lebanon. In frustration, Curran visits Verrons' to plead for her help. She finally agrees to cooperate as long as she only answers questions, but does not volunteer information. Curran, Hawkins, and Verrons meet on Curran's houseboat to discuss questions Curran has provided. Claire provides information on a source that could lead the SEALs to the location of the missiles. Curran presents the new information to the same group of military and civilian men he faced before. A civilian member of the group identifies the informant as a known information merchant. The SEALs are authorized to kidnap the informant.
The Team meets at their command center to work out the details for the kidnapping. They agree with Captain Dunne that the mission should be an easy one, with possibly no shots fired. They arrive at the targeted house, having deployed by parachute from twelve miles up and swimming in, but as Curran leads several of the team in to kidnap the man, Hawkins is left to lead the three men remaining in the street as backup. When one SEAL is pinned down by soldiers in the street, Hawkins disobeys Curran's order to stay quiet and unmoving. His reckless action succeeds in getting the soldiers killed, but in their confrontation, Bill Graham is killed. It is clear that Graham was Curran's best friend.
The duty of informing Graham's fiancée of the man's death falls to Curran. After a military funeral for his friend, Curran comforts Graham's fiancee again,, but he refuses to answer her questions about how Graham died. The team meets at a local bar, The Ready Room, for a wake for the Chief. Curran is drinking heavily, and they all are watching a video of the golf outing they had recently enjoyed. After fighting with a local drunk, Hawkins makes a toast to Graham. Curran is furious with the other man and walks out. When Hawkins follows, Curran turns on him and accuses Hawkins of "toasting a man he put in the grave." When Curran walks away, Hawkins finally admits to himself that the death was his fault, but he seems to have trouble dealing with the guilt.
At the harbor, Claire Verrons appears at Curran's houseboat, surprised to find the place totally wrecked. She finds Curran on the upper deck, mourning for his friend. They walk on the boardwalk, and Curran tells the woman about the mission. Her wanting to comfort him, he in need of comfort, they wind up sharing the night in Curran's bed. She wakes to find him already dressed and preparing the leave. Curran tells her that the informant has provided key information on finding the missiles, and leaves her there as he goes on mission again.
The new deed begins. The Team uses pontoons to enter Beirut, this time met by an AMAL guide to lead them inland. The guide turns out to be a cigarette smoking, machine gun toting teenager. Many military factions are at war in the city, and the team must navigate among them to reach their target. Wanting no part of the warfare, they attempt to evade all the groups, but at last are pinned down. The team sharpshooter, Dane, attempts to find a high ground location to help them get past the warring men. However, Dane is shot and killed, but not until he saves Curran from being shot in the back.
The team, still led by the young AMAL scout, finally reaches their target. The missiles are stored in an old school building in a heavily bombed area of the city. The AMAL scout leaves them to their work, slipping away into the night. After spending the remainder of a sleepless watch huddled among the ruins, the team disperses. Of the five remaining SEALs, Curran, Leary, and Rexer take explosives into the schoolhouse to destroy the missiles. Hawkins and Ramos, the communications specialist, wait outside to provide backup and cover for the other SEALs. Curran leaves the detonator for the explosives with Hawkins.
The explosives are set but, as the three men leave the schoolhouse, shots ring out from the upper floor of the school building. Shaheed, with a numbers of his soldiers, are using the top part of the building as a make-shift headquarters. Curran is shot as the other two from his group join Hawkins and Ramos.
Although lying in harm's way, Curran gives a direct order for Hawkins to blow up the building. Knowing to carry out the order would mean Curran's death, Hawkins refuses to let another friend die. He leaves the detonator with Ramos, and in a daredevil, heroic move, he pulls Curran from the front steps of the building, giving the order to destroy the building at last.
Now the SEALs must escape and meet their extraction transportation, a Navy submarine. Carrying a badly wounded Curran, who is high on morphine, the Team steals an automobile and make a break for the beach. They are soon spotted by a tank emblazoned with the name of a Middle Eastern group. The team race through the streets, unsure of the location of the beach, with the tank forever on their trail. The automobile is finally shelled and flipped onto its top. As they extract themselves and the wounded Curran from the car, Hawkins and the others realize they have lost another friend. Rexer has been killed. The men scramble away from the burning car on foot, still trying to reach the beach and extraction. They know that they are late.
Although they have managed to destroy the tank, they are now pursued by Shaheed and his soldiers. Even reaching the safety of the Mediterranean Sea, the team is followed. First the pursuers fire machine guns at the fleeing men, then fire a missile into the water close to where the SEALs are diving to escape.
Shaheed steals a boat from a pier-side fisherman, and follows the SEALs across the water. He spots the form of a SEAL floating in the sea. As he attempts to pull the body from the water, he is attacked by the SEALs, and in an underwater fight, Hawkins kills Shaheed. The other SEALs take out the remaining topside terrorists and destroy the small boat.
As the movie closes, the remaining members of the Team are seen adrift in the sea, hoping, but not certain, that the extraction submarine will return to take them home. Suddenly the submarine surfaces beneath them; Curran's commander having persuaded the submarine captain to turn back and make one last sweep of the area.