As Su A recovers in the hospital following the attack during the break-in, Hae Seong and the team uncover the culprit: Lee Jun Ho, the mathematics teacher. When Hae Seong detects his father's notebook missing, he realizes that Seo Myeong Ju 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 Seong stumbles upon a crucial clue to the final scary story.

To everyone's shock, Seo Myeong Ju returns to the school. Unimpressed by Hae Seong, she expels him and demonstrates her power by dismantling his team. However, refusing to back down, Hae Seong and the team, including Su A and her mother, devise a daring plan to infiltrate the school once more to retrieve the hidden gold bars

Despite getting badly injured, Hae Seong manages to call Su A 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 Myeong Ju decides to take a special measure to end everything.

The gold bars vanish just as they are within reach, and Seo Myeong Ju suspects Hae Seong has them. In the vault, Hae Seong 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 Seong heads to confront him alone.

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 Seong 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 Su A witnessed it all

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

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

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.