Ray, Jason and Bravo team are on an arms control mission to rescue American captors from a group of extremists on an oil rig in the Gulf of Guinea. After Ray clashes with Jason, who is suspicious of him, Ray thinks about joining another SEAL team.
SEAL team head to Saudi Arabia to deal with a terrorist bigots, who are threatening to release anthrax into the main pipe of a water main. Despite that Jason loses track of Sonny, they reunite and deal with the terrorist who threatens to bomb the tunnel.
To his dismay, Jason relinquishes his position in Bravo team for the sake of his children, and passes the baton to his SEAL teammate, Adam Seaver.
In a hotel in Mumbai, the team manage to save the seized Diplomatic officer from his bigot abductors, and they are then called for another mission. Jason stays with his children and reconsiders his upbringing of them.
While at a local university in Mumbai, the team tries to save captive American students from an act of terrorism. A bombing occurs and Adam dies, but the rest of the team deals with the terrorists and end their lives. Jason is back to Adam's funeral.
The team travels to Mexico to search for the lethal drug kingpin, Andres Doza, who has murdered an official working at the Drug Enforcement Administration, in association with the Mexican Marines.
Bravo Team keeps track of a businessman who works with Andres Doza in the cartel. To their surprise, the businessman is killed before they could reach him, after which they decide to kidnap the CEO of a company that deals with the cartel.
Jason and Mandy go incognito to a nightclub in Mexico, at which the CEO spends the night. After they detain him, Jason and Mandy question the CEO, who informs them of the whereabouts of Doza's best friend, Castillo, whom they decide to keep track of.
On surveilling Castillo, the team is attacked and they doubt the presence of a betrayer among them, that turns out to be Rita. While Castillo breathes his last, he informs Ray of Doza’s whereabouts.
SEAL team arrives at Doza's hideout mansion, and they arrest him. Colonel Lopez is forced to put Doza to death and agrees with Jason to state that Doza has committed suicide so that Col. Lopez won't get excluded from the prosecution.
As a plane, en route from Tunis to Barcelona, is hijacked by a group of extremists in Doha airport, the team cooperates with the British SAS to rescue the passengers. Jason dismantles the plane's undercarriage and saves the situation.
Bravo Team is summoned to Turkey when an American woman, married to an ISIS terrorist, is kidnaped by the terrorist group, and they must get her out of a mausoleum guarded by outnumbered standing sentinels.
On a submarine near the coast of North Korea, Sonny is stuck in a torpedo tube when the team suspects an Iranian shipment. Sonny starts to suffocate as the tube swamps, so the team reaches out for the submarine's captain who opens the tube and saves Sonny.
The team heads to Congo to track down a mob boss who killed Americans while building a hospital, and they arrest him with the help of the Congolese Army. Lisa decides to give Sonny a chance in their relationship. Jason understands Emma's needs and agrees that she goes to study in New York.
The team is sent on a special mission to catch a terrorist member, whom they try to keep track of, and are shocked that he has changed his location. But when they're spotted and exposed, Bravo Team is attacked by the townspeople until the marine troops save them.
Bravo Team heads to the Philippines to train their fellow SEALs. An airplane crashes near South China Sea, and the team is called for investigations. Jason struggles to pay Emma's college fees.
Bravo Team take their fellow Filipino SEALs on a mission on an oil platform. While in a bar in Manila, the team encounters a bombing that leaves Clay injured with wounds that threaten to end his life.
Even though Clay's health improves, his right leg is severely injured, leaving him distressed whether he can get back to work with the team again. Mandy finds the criminals who bombed the bar, after which the team raids their hideout and arrests the mob boss.
Bravo Team travels to Mali on a special operations mission, where they meet up with Brett Swann, their former fellow SEAL, whom Clay takes to the hospital to treat his brain injury, but when the administration refuses, Swann shoots himself at the parking lot.
Ray and Jason gets into a fight in the Guam base, after they rain blows on each other in a bar. Lisa must enter the fire emergency test to graduate from the OCS. Bravo Team is called for the port of Bangkok to put an end to an attack.
In a territory in Northern Pakistan, Bravo Team loses contact with Ray, who accidentally landed in the enemy territory. By the help of the Indian authorities, Bravo Team saves Ray, and an Indian Air Force helicopter safeguards them.
Because they failed the mission, Commander Shaw decides that Bravo Team breaks up. To prove him wrong, the team manage to capture Khan, one of the most dangerous terrorists, and kill four of his partners. Clay and Stella get engaged. Jason puts his house on sale and joins Emma in New York.