The story is not linked to the first part of the series. Instead, it focuses on a fictional explanation for the Ryanggang explosion in 2004, in which an unexplained mushroom cloud occurred in North Korea.
The Pentagon aborts the mission after receiving new information, but by the time the abort order is sent, two SEALs have already parachuted into North Korean territory. James stops the third SEAL from deploying, accidentally knocking the man's helmet against the status indicator mounted near the door. He steps onto the makeshift ramp to peer outside, returning to the doorway to inform the other men of the abort. The high-speed winds from outside rip the indicator loose and send it flying into his face. Stumbling backwards, James loses his balance and is blown out of the plane. Master Chief Neil T. "Spaz" Callaghan (Matt Bushell) disobeys orders to stand fast, strikes his commanding officer, and follows the first three, taking a radio with him. When North Korean forces led by Commander Hwang (Joseph Steven Yang) find the SEALs, they kill two in a gun battle, and Hwang and his men capture and torture James and Callaghan.
After South Koreanspecial forces rescue the pair, President Manning and the South Korean government send the SEALs and South Korean special forces to destroy the missile site. But after losing radio contact with the SEALs, the President and his top advisers believe that they have been captured again. Under pressure from his Chairman of the Joint Chiefs of Staff, US Air Force General Norman T. Vance (Bruce McGill), the President decides to send B-2 stealth bombers to destroy the site, which would start a full-scale war against North Korea. Hwang almost recaptures the SEALs and the South Korean special forces, but a defecting officer shoots him. James and the South Koreans destroy the missile silo with a bomb before the bombers reach the missile site, which averts the bombing and prevents a full-scale war.
A tribunal convicts Callaghan of striking an officer (1 year) and disobeying an officer (10 years). Due to the mission's "black op" nature, the transcript of the hearing is deemed classified and the charges are expunged from his record, freeing him to return to his family.
Meanwhile, James meets the president in a classified meeting, bringing his mentor Master Chief Scott Boytano (Keith David) to witness James receive an award. The film closes with Boytano telling James he was not red flagged because Boytano had never seen anyone who desired so badly as James did to be a SEAL. During the credits there is a news report on the Ryanggang explosion.
The film followed on the footsteps of a previously released title: Behind Enemy Lines, starring Owen Wilson. Although the basic theme is credited to the first film, the plot and setting are not interlinked between either films.
