The story begins with when Tino, a prince of the merfolk, meets Lucia, a young woman from a fishing village. Enraged by the destruction wrought by some fishermen on marine life, Tino vows revenge on humans. He has a change of heart, however, when he witnesses Lucia and her father arguing with a group against using dynamites to fish. When a dynamite accidentally explodes at the height of the exchange, sending Lucia and her father plunging into the seawater, Tino decides to save them both by bringing them to the shore. While Lucia survives, her father dies due to injuries from the blast. Drawn to the young woman, Tino once again swims near the shore, only to see Lucia grieving. Tino initially looks on from a distance, but decides to show himself when Lucia catches a glimpse of him and requests that she be given the chance to thank him. At first shocked to see Tino's tail, Lucia remembers his efforts to save her and her father. She returns to the beach after initially fleeing, and sits beside Tino to talk about her life, as he does. After Haring Aurelio banishes Prince Tino from their kingdom, Prince Tino goes back to Lucia. He tells her that he doesn’t regret his decision. He says he will always choose his family because he loves them dearly. Soon, Lucia goes into labor gives birth to a baby girl. Lucia and Tino are overjoyed and name the baby Beatriz after Lucia's mother. One night when Beatriz won't stop crying and Tino is nowhere to be found, Lucia goes to the banca, intending to bring Beatriz to the hospital on her own. When Beatriz's feet gets wet with seawater, her legs turn into a fish tail. Only the magic conch-shell can turn the baby's tail back to its normal feet. Although surprised by their daughter's strange form, they promise to love their child no matter what. But in no time at all, their neighbors discovered the couple's secret. When the community is hit with a series of catastrophes, the town believes that the anomaly is caused by Dyesebel; an accusation that leads to Prince Tino's death. Before her father is killed by an angry, superstitious mob, Dyesebel is taken to the ocean by him through Banak where she is sent into exile since her chances for survival are greater there than on land.
Years have passed, little Dyesebel goes near the shore and a bottle lands on her head. She inspects the bottle and she grows curious about the piece of plastic on her hand. Fredo, meanwhile, thinks he saw a little girl in the water. Dyesebel goes back home and finds Banak panicking because she is nowhere to be found. Banak scolds Dyesebel for making her worry. She scolds Dyesebel more when she finds out she went to the shallow waters. Banak remembers what happened to Prince Tino. She tells Dyesebel that the people will kill her if they capture her. Dyesebel calms Banak down and tells her not to worry anymore because she's safe. She also promises not to go back to the shallow waters. Days later, Dyesebel saves Fredo from drowning during a tsunami wave. She befriends Fredo without revealing that she's a mermaid. Fredo talks to Betty and tells her about his friend Dyesebel. He tells Betty that Dyesebel is always in the water. Dyesebel, meanwhile, talks to Liro and tells him about Fredo. She tells him not to be afraid of humans because she has met a good human in Fredo. Later, Dyesebel also talks to her sea friends and reveals to them her secret. She sings to let them know that she has an unseemly voice. The other mermaids hear her singing and mock her voice. Dyesebel is very sad and she swims away to a place where she can be alone. She stays there and sings all by herself. After some years have passed, Dyesebel went swimming freely in the sea, now all grown up and very beautiful. Likewise, Fredo, Liro, and Betty have now grown into adults. Dyesebel decides to let go of her memories of Fredo. She goes to the place where she last saw young Fredo to return the bottle he left for her. When she's near the shore, Fredo is there looking out to the sea and shouting in frustration. Dyesebel thinks he's weird and she says so. Fredo hears the voice and swims towards it. While he doesn't see anyone, what Fredo sees amazes him even more. He sees the bottle he left for Dyesebel. He calls out her name and he dives into the sea to look for her. Fredo doesn’t see her but he is happy because this time he knows that Dyesebel is not a figment of his imagination. This time he will do everything to look for Dyesebel.
Reyna Dyangga pins Ginang Orca's death on Dyesebel and she makes sure the whole kingdom knows that Dyesebel is the daughter of prince Tino and a human. This is unacceptable to most of the kingdom and they decide that Banak and Dyesebel should die. In the morning, Dyesebel and Banak are released in an area inhabited by deadly sea monsters. Dyesebel and Banak plan on fighting the sea monsters and escape. They escape the sea monsters. Dyesebel goes straight to where the magic conch-shell is hidden and she manages to sneak in and get it. She is also able to defeat the soldiers of Reyna Dyangga. However, she loses sight of Banak, who is by that time, being captured by fishermen. Dyesebel immediately swims ashore and begs the magic conch-shell to help her. She rubs the shell and her tail transforms into human legs. Dyesebel is helped by a couple and given clothes. The man brings her to Manila and Dyesebel somehow senses that the man has bad intentions towards her. Indeed, the man is selling Dyesebel to several men. She finds a chance to escape from the men. She wanders alone in Manila. She is confused by the noise and multitude of people in the city. She wanders some more until she ends up in the middle of the street. A car stops short of running her over. Fredo comes out of his car and stops when he sees Dyesebel, captivated by her beauty. Fredo saves Dyesebel from the men holding her captive. They also help the other women captured by these men. However as they are about to leave the house, a group of men accost them. Luckily, Fredo's friends arrive and help them beat up the men. Fredo hears Dyesebel mention her name to the police. Fredo asks Dyesebel if she has met a boy on the shore when she was a kid. Dyesebel nods and asks if he is Fredo. They hug each other, very happy to find each other at last. When Fredo sees fishermen cast a net over Dyesebel, he dives in and helps her get out of the net. They swim ashore and Fredo ties a shirt around Dyesebel's wounded tail. Fredo learns of Dyesebel's search for Banak and he promises he will help her get back her magic conch-shell so that they could find Banak. But first, they have to tend to Dyesebel's wounds. Fredo also finds out that Dyesebel's real mother is human. Fredo then tells her that he is willing to fight for their love, no matter the cost, just like Dyesebel's parents fought for each other. Fredo overrides all her protests until Dyesebel promises Fredo.
Lucia spills what she believes is seawater on Dyesebel's legs, but Dyesebel's legs do not turn into a mermaid's tail. After leaving Dyesebel, Lucia cries in disappointment. Liro sees everything that happened and he suspects that Lucia is Dyesebel's mother. Liro pays an old man to tell Lucia that a baby mermaid died in his care after a man left her to him. He shows Lucia where the baby is buried. Lucia opens a small wooden coffin and it has a skeleton of a baby mermaid with a shell necklace on top. She cries because this time she is sure that Dyesebel is dead. She buries the remains of the baby mermaid whom she believes to be Beatriz. Dyesebel goes to the burial to console Lucia. After Lucia leaves, Dyesebel goes to Beatriz's tomb to pay her respects and she sees a shell necklace beside it. It is the same necklace that links her to her mother. Dyesebel cries as she remembers all the clues that tell her that Lucia could be her mother. She goes to Banak and Banak confirms her suspicion. Dyesebel accuses Banak of lying to her again and she runs away from Banak. Lucia is about to be killed by a group of mermen and he asks them why they are doing this. They tell her that they captured her so that Dyesebel would return the magic conch-shell. Now that they have it, they have no more use for her. Lucia is confused and the mermen mock her ignorance. Lucia thinks some more until the truth dawns on her: Dyesebel is her daughter, her missing Beatriz. Pinky and Karlo help her escape the mermen. Dante and Fredo, with a group of seamen, also come to her rescue. Dyesebel wakes up with Lucia sleeping beside her. Lucia opens her eyes and hugs Dyesebel tightly. Dyesebel cries and tells her mother that she wants to call her as mother. Meanwhile, Betty finds a way to know what Lucia is keeping secret from her. When she learns that Dyesebel is no other than Beatriz, she screams in anger and disbelief.
While walking down the aisle in her beautiful wedding gown, Betty approaches Dyesebel and spills seawater on Dyesebel's legs. Dyesebel's legs turn into a mermaid tail. Angry people swarm around Dyesebel and beat her up. Lucia and Banak can do nothing to stop the people from beating Dyesebel. Fredo becomes bloodied in his attempt to save Dyesebel. Liro uses his merman shout to clear the people away from Dyesebel, but men from the Bantay Dagat shoot Liro and carry Dyesebel away. Dante Montilla died while trying to help his son Fredo save Dyesebel. Dyesebel and Fredo exchange wedding vows in front of Lucia, Banak, and their loyal friends. Fredo tells Dyesebel that he doesn't regret even their painful memories because it brought him to Dyesebel, while Dyesebel professes to do what she can to bring peace to their relationship and their lives. With the help of his cousins, Liro gets the magic conch-shell from Reyna Dyangga and he uses it to fight Dyangga's men. Liro goes to Dyesebel and gives her the magic conch-shell. He tells her that she is the rightful heiress to the King's throne and that they need her help under the sea. Dyesebel eventually decides to fulfill her duties as queen of their kingdom. Dyesebel sought to finally end the war between her people and those on land by seeking dialogue with the human government. This, after a string of casualties from the hostilities, including Stella and Dante. Ena regrets her evil deeds. She goes to Lucia and asks her forgiveness. Betty also begs forgiveness from Dyesebel.
Now recognized as the rightful queen of the merfolk, Dyesebel led her kind to a cave where the first blood in the long-waged war was shed. Here, she negotiated with humans to put an end to their destructive ways of fishing, which has long been the reason for mermaids' animosity toward them. Dyesebel pushes for a peace treaty between humans and mermen. However, Dyangga gets in the way and causes a violent encounter between human and mermen soldiers. In an attempt to sabotage Dyesebel's efforts, the ousted queen triggered fighting once more with the help of her henchman, Kanor. Liro, Dyesebel's childhood friend, was killed after taking a bullet for her. The loss of a loyal soldier pushed Dyesebel to make a desperate plea to stop the fighting, this time by physically tackling the warring sides and putting herself in harm's way. When Coralia, Dyangga's daughter who had bullied Dyesebel as a child, was caught in the sight of a human soldier, Dyesebel did not hesitate to plunge into the water to save her from a gunshot. Dyangga, captured by humans, could only look on as the mermaid she has hated for so long took a bullet for her daughter. For Dyesebel, it was the ultimate sacrifice—risking her life for the same family who had plotted the assassination of her father, Tino, to seize his throne. Dyesebel's sacrifice silences the opposing groups, and both men and mermen, carry Dyesebel towards the hospital. With Dyesebel in critical condition, her human mother, Lucia, made a televised appeal to put an end to the war before there are any more casualties on either side. After an apparent jump in time, Dyesebel was seen swimming in her kingdom and, later, freely walking on land—a sign that a truce between humans and mermaids had finally been reached. Here, she was welcomed by Lucia and Fredo, as well as a little girl who appeared to be her own.