In the climactic episode of The WONDERfools, we find Chae-ni and Gyeon-un attempting to escape the church. Gyeon-un is filled with anxiety about his family, but Chae-ni urges him to focus on their escape as the churchgoers close in. Using the last of her coffee jelly, she teleports them both, leaving Gyeon-un safely outside his house.
Returning to the church, Chae-ni confronts the crowd with a chainsaw, only to have it break accidentally. The churchgoers attack her, but Jun-mo and Jeon-bok burst into the church, using a speaker system to disrupt Ju-ran's brainwashing spell and stop the church members from acting like zombies.
Meanwhile, in the basement lab, Un-jeong confronts Dr. Ha, who has ruined his life through experiments conducted on him as a child. Dr. Ha refuses to accept responsibility and claims that Un-jeong should stop blaming him for everything. He reveals his plan to spread chemicals throughout Haeseong to create more people with superpowers and increase the chances of producing another Child of Eternity. Un-jeong tries to kill Dr. Ha, but the guards attempt to shoot him. Using his powers, Un-jeong controls the bullets and turns them back on Dr. Ha, killing him while also setting the lab on fire. Chae-ni hears the explosion and panics. She teleports into the lab, rescues the people trapped inside, and desperately searches for Un-jeong.
At the same time, Ju-ran attempts to revive Dr. Ha using Chae-ni's blood sample but fails. She contacts Ho-ran and tells her to make sure everything continues as planned, hiding the truth about Pal-ho and Dr. Ha's deaths from her. Elsewhere, Sang-moo drags an injured Un-jeong out of the burning lab and urges him to escape.
Outside the church, Chae-ni tells Jeon-bok and Jun-mo about Dr. Ha's apocalypse plan. Just then, Ho-ran appears and brainwashes Jun-mo along with his team, forcing them to target Jeon-bok. Chae-ni quickly teleports Jeon-bok away to save her life. Since she remains attached to the church, she accidentally teleports back there, this time arriving on a telehandler. Chae-ni tries to threaten the brainwashed people so they will stop attacking her.
This episode marks a turning point in the story of The WONDERfools, as characters face difficult choices and unexpected twists that will shape their futures.
As the midnight parade to celebrate the new millennium approaches, Gyeon-un rushes to City Hall to prevent Mi-hui and Cheong from attending. His efforts, however, are met with resistance; they refuse to listen to him, with Cheong feeling embarrassed by his desperate attempts.
Later, Chae-ni, Ro-bin, and Gyeon-un regroup at a restaurant to discuss their next move. Gyeon-un realizes that Ho-ran plans to release the chemicals during the parade when the entire town will be gathered. Chae-ni and Ro-bin set out to find the truck carrying the chemicals, but they encounter Un-jeong under Ju-ran's control.
Ju-ran forces Un-jeong to attack Chae-ni, but Ro-bin uses his powers to shield her. Gyeon-un stays near the parade, determined to protect his wife and daughter. When he hears about the fireworks display planned for midnight, he realizes that the chemicals will be spread through the fireworks.
As chaos erupts, Ro-bin and Un-jeong engage in a fierce fight, while Gyeon-un races to protect his family. Ju-ran forces Un-jeong to strangle Chae-ni, but Chae-ni teleports him away to break Ho-ran's control over him. Meanwhile, Ho-ran begins brainwashing other residents of Haeseong, but Chae-ni and Un-jeong quickly return to the city.
Gyeon-un tells Mi-hui and Cheong to hide before rushing back to help his friends. Together, they use their powers to battle the brainwashed townspeople under Ho-ran's control. Cheong watches everything unfold and finally realizes that her father is a real superhero.
With only thirty minutes left before midnight, the group splits up to search for Ju-ran and stop her plan. Gyeon-un confronts Ju-ran but is thrown off a building by her. As Ju-ran weakens from overusing her powers, she collapses. Ho-ran panics and desperately tries to help her.
As Ju-ran weakens further, the brainwashing spell wears off, and the townspeople regain control of themselves. Meanwhile, Ho-ran uses her hallucination powers and disguises herself as Chae-ni in an attempt to kill Un-jeong. However, a church elder stabs Ho-ran during the confusion. The illusion fades, and Ho-ran dies in Un-jeong's arms as Ju-ran watches in horror.
Ju-ran casts one final spell on the entire town, forcing everyone to gather beneath a blimp carrying the chemicals. Un-jeong tries using his powers to stop it but is too weak. Chae-ni asks Ro-bin and Gyeon-un to launch her toward the blimp while Un-jeong promises to stop her from falling.
The tale of Do Chae-ni and her friends' triumph over Dr. Ha's apocalyptic scheme unfolds in a series of dramatic, heart-pumping events. Gyeon-un assists Chae-ni in scaling the blimp, then jumps back down, while Un-jeong saves Gyeon-un from a crash. Chae-ni, at the eleventh hour, teleports the blimp away, saving the day. Ju-ran finally surrenders, and the spell over the townspeople vanishes.
As midnight strikes, the residents of Haeseong celebrate the dawn of a new millennium. Meanwhile, Jeon-bok, Un-jeong, Ro-bin, and Gyeon-un are left to ponder Chae-ni's disappearance.
The season finale of "The WONDERfools" brings a poignant conclusion. Three weeks pass with no sign of Chae-ni, leaving her loved ones in a state of deep concern. Jeon-bok and the others organize a memorial in her honor.
During the solemn ceremony, Chae-ni makes a surprise appearance, reuniting with her family and friends. Un-jeong learns of her return and rushes to find her. The two embrace, symbolizing their reunion. The season ends with Chae-ni, Un-jeong, Ro-bin, and Gyeon-un continuing their bond of friendship.
An epilogue adds depth to the story, showing Un-jeong dreaming of reuniting with his mother while the Church of Eternal Salvation faces investigation. Meanwhile, Dr. Ha awakens in the underground lab, leaving room for future adventures and suspense.
