In the third episode of The WONDERfools, we're introduced to Nam Sun-gyu, a man who meets Dr. Ha Won-do in prison. The scientist is questioned about the Child of Eternity, and Sun-gyu informs him that Un-jeong has returned to Haeseong. To aid in the search for Un-jeong, Sun-gyu helps Won-do escape from prison.
The episode then picks up where the previous one left off, with Chae-ni making it back to Haeseong from the boat where she was nearly shot. She suddenly appears in front of Un-jeong, startling him, and he pushes her away with great force.
Meanwhile, Seok Ju-ran, Seok Ho-ran, and Kim Pal-ho, all loyal followers of Dr. Ha, discuss Un-jeong's return to Haeseong. Ho-ran recalls how Pal-ho used to be jealous of Un-jeong, while the trio talks about his sudden reappearance. Dr. Ha instructs them to capture the new variant, Chae-ni, before she becomes a bigger problem for him.
Elsewhere, Gyeon-un leaves Chae-ni at Ro-bin's house after she passes out. When she regains consciousness, Chae-ni reveals that she can teleport, leaving Ro-bin shocked. At the same time, Gyeon-un's wife, Mi-hui, gets angry at him for failing to complete the flower deliveries on time. Gyeon-un attempts to lie to her but ends up getting his hands stuck to a flower pot.
Later, Chae-ni and Ro-bin visit the flower shop to speak with Gyeon-un while Un-jeong's superior, Seok-u, pressures him for updates on the investigation. Chae-ni and Ro-bin try to discuss their powers with Gyeon-un, but he refuses to cooperate. Moments later, Gyeon-un's feet suddenly become stuck to the floor, preventing him from moving.
Chae-ni insists that all of them now have superpowers, but Gyeon-un does not want anyone finding out about his strange ability to stick to random objects. He eventually reveals that Un-jeong tried to kill Chae-ni at the warehouse.
The next day, Chae-ni shows up at City Hall and tries to get Un-jeong to speak with her privately. The employees at the Civil Complaints office become nosy as the two continue arguing in front of everyone. Un-jeong asks Seok-u to help him escape the situation.
Around the same time, Na-yeong brings up a stench complaint from Haedeul. Un-jeong volunteers to investigate the matter so he can get away from Chae-ni. Chae-ni then asks Gyeon-un to chase after Un-jeong before he escapes.
Meanwhile, the police ask Jeon-bok to identify Director Choi's body at the morgue. They hand her his suicide note, in which he claims that Dr. Ha Wondo is innocent. A flashback reveals Director Choi coercing Dr. Ha into revealing the location of the Child of Eternity. Ju-ran uses her powers to force him to reveal the information. Assuming that Chae-ni is the child Jeon-bok once mentioned, Director Choi tells the scientist about Jeon-bok's restaurant, Hearty House. Ju-ran then forces Director Choi to stab himself with a pen.
In the present day, Dr. Ha awakes from a nightmare of the fire at Hawondo Lab years ago, recalling the children fleeing while he was arrested for conducting illegal experiments on minors.
The next day, two police officers, Park Seung-ryeol and Gyeong-hwan, arrive at the Hawondo Church of Eternal Salvation after receiving a missing persons complaint involving Sang-moo. Ju-ran escorts the officers through the building while they request access to the basement.
However, despite Bong-pal and Sang-moo's desperate cries for help, Ju-ran uses her powers to prevent the cops from hearing them. Later, inside the police car, Seung-ryeol notices something sticky on Gyeong-hwan's face and comments on it.
At the same time, Chae-ni, Gyeon-un, and Ro-bin trick Un-jeong into getting inside their car. They question him about their powers, but he refuses to explain anything. Suddenly, the police car approaches them, and Gyeong-hwan's face begins to melt off before he crashes the vehicle.
Chae-ni, Ro-bin, and Gyeon-un rush to rescue the officers. They manage to pull Seung-ryeol out safely but struggle to rescue Gyeong-hwan due to his wobbly and boneless body. Chae-ni begs Un-jeong for help, and he reluctantly uses his powers to lift the car.
Gyeon-un brings water to prevent the vehicle from catching fire but accidentally gets himself stuck to it. Ro-bin and Chae-ni desperately try to help him while the flames continue to spread. Chae-ni teleports away to find a sickle so they can cut Gyeon-un's arm free.
However, before she returns, Ro-bin uses his super strength to pull Gyeon-un away moments before the car explodes. Chae-ni returns and feels relieved after seeing that Gyeon-un survived.
Elsewhere, Jun-mo informs Jeon-bok that the CCTV footage from Director Choi's house has been erased. Concerned for her safety, he urges her to go into hiding.
Meanwhile, on the drive back, Chae-ni excitedly claims that the four of them are now a team. However, Un-jeong refuses to be associated with them. Gyeon-un, Ro-bin, and Chae-ni discuss claiming a government reward for saving the officers' lives.
Meanwhile, Un-jeong tries to piece together the strange incidents happening around Haeseong and concludes that the Church of Eternal Salvation is somehow involved.
Elsewhere, Chae-ni, Gyeon-un, and Ro-bin attempt to officially report the accident involving the cops. However, they realize that someone is trying to cover up the truth about the incident, which leaves them worried for their safety. Chae-ni then decides to confront Un-jeong again.
At the same time, Pal-ho confronts Un-jeong at City Hall and questions why he returned to Haeseong. Un-jeong mocks Pal-ho for calling Dr. Ha "Father" and accuses the scientist of using defective variants like them for his own benefit. He insists that Dr. Ha does not actually care about them. Although Pal-ho becomes furious, Un-jeong tells him to leave.
Later, Chae-ni tracks Un-jeong down at work and asks him to take her, Robin, and Gyeon-un under his wing while also answering questions about their powers. Un-jeong asks whether she knows anything about the "Wunderkinder" but refuses to explain further. When a colleague suddenly appears, Un-jeong uses his powers to hide Chae-ni from sight.
Un-jeong later reveals that he also had a near-death experience when he first gained his abilities. He reassures Chae-ni that she no longer needs to fear death. Chae-ni happily leaves City Hall, but Un-jeong notices Pal-ho secretly following her. Just as Pal-ho prepares to attack Chae-ni, Un-jeong arrives in time to save her.
Afterwards, Un-jeong decides to keep Chae-ni close to him and calls her back. He asks her to join a team working for City Hall. At the office, Un-jeong hires Chae-ni as a temporary paid volunteer. Chae-ni excitedly calls Jeon-bok to tell her about the job, which makes the old woman happy. However, once Jeon-bok returns to her restaurant, she is greeted by Dr. Ha, as the episode comes to an end.
