After a botched operation puts Hae-sung and his team in serious jeopardy, the only way for him to salvage his career at the NIS is to accept an assignment that seems almost hard to believe. Hae-sung and his team must infiltrate Byeongmun High School, one of Korea's most elite private institutions, to recover ten tons of gold bars worth a staggering 80 million dollars. With everything on the line, Hae-sung puts on a school uniform, and "Operation Undercover High School" begins.

Hae-sung comes dangerously close to blowing his cover while searching for the hidden gold in Byeongmun High School's eerie old building, barely escaping detection by Soo-ah, his sharp-eyed homeroom teacher. As he hears chilling rumors and faces tight security surrounding the building, he believes that's where he'll find the gold. While dealing with school bullies, Hae-sung begins plotting his next move to uncover the dark secrets lurking inside the old building.

Hae-sung uncovers a crucial clue hidden within the old building, but Chairwoman Seo quickly learns its potential connection to the elusive gold bars. Sensing the connection, she keeps Hae-sung under close watch. Meanwhile, as Hae-sung delves deeper into the ghost stories surrounding the school, he finds himself caught in the escalating tension between Tae-soo and Dong-min, whose conflict ignites chaos throughout the school.

Hae-sung attends the anti-bullying committee session with a key witness who clears his name, while Dong-min finally finds the courage to stand up for himself. With his name vindicated, Hae-sung uncovers the existence of another grandfather clock hidden in the student council room, and the only way to get closer to it is by joining the student council. With the help of his team, he tries to meet the strict requirements.

Hae Seong and the team grow increasingly concerned that Su A's suspicions could threaten his undercover mission. However, Hae Seong defies the odds and successfully gains a spot in the student council. With this new role, his focus shifts to unraveling the mystery behind the old clocks. Meanwhile, a shadowy figure emerges, threatening to expose Hae Seong's true identity.

The school's security guard dies, leaving Hae-sung a notebook belonging to his missing father. The revelation is shocking, and he storms the NIS for answers. The answer pushes him away from the mission, and he takes time off. However, he resolves to continue but returns only to discover Soo-ah witnessed it all.

Hae-sung is caught off guard when he recognises Soo-ah's childhood name, Bong-ja, which stirs memories of his first love and distracts him from his focus. Despite the emotional turmoil, Hae-sung pushes forward with the mission to uncover the secrets behind the third ghost story. However, a missing key component forces Soo-ah to join the mission despite Hae-sung's strong opposition to her involvement.

After uncovering the possibility of a mole within the NIS, Hae-sung becomes increasingly distrustful of those around him, causing him to question the mission's integrity. Meanwhile, Soo-ah exposes a secretive scheme within the school that guarantees top grades for VIP students. As the web of secrets deepens, Hae-sung uncovers the connection between the gold bars and Chairwoman Seo, prompting him to vow to end her sinister plans.

As Soo-ah recovers in the hospital following the attack during the break-in, Hae-sung and the team uncover the culprit: Lee Jun-ho, the mathematics teacher. When Hae-sung detects his father's notebook missing, he realizes that Seo Myung-joo orchestrated the break-in. After Lee Jun-ho's arrest and confession, the revelation of the school's grade-rigging scandal throws the institution into chaos. Amid the turmoil, Hae-sung stumbles upon a crucial clue to the final scary story.

To everyone's shock, Seo Myung-joo returns to the school. Unimpressed by Hae-sung, she expels him and demonstrates her power by dismantling his team. However, refusing to back down, Hae-sung and the team, including Soo-ah and her mother, devise a daring plan to infiltrate the school once more to retrieve the hidden gold bars.

The gold bars vanish just as they are within reach, and Seo Myung-joo suspects Hae-sung has them. In the vault, Hae-sung makes a heartbreaking discovery of his father's remains. Overcome with grief, he finally finds closure, but a shocking truth emerges. He learns Director Kim Hyung-bae was behind it all. Determined to uncover the whole story, Hae-sung heads to confront him alone.

Despite getting badly injured, Hae-sung manages to call Soo-ah and his team. They conclude that the only evidence they can secure is the flash drive that contains the voice recording of Principal Park murdering Director Kim Hyung-bae. After finding out that an arrest warrant had been issued for her, Seo Myung-joo decides to take a special measure to end everything.