In 1118 in Kyoto amid the time of confusion, Taira no Tadamori, the heir of the Taira clan, spends days doing dirty works to capture robbers under orders of the Imperial Court. One day, he encounters a pregnant woman named Maiko, who is on the run to protect her unborn baby, a child of the cloistered Emperor Shirakawa (who although retired is still the most powerful,) from being murdered. Tadamori secretly provides shelter to Maiko, while shaking off the pursuit from Minamoto no Tameyoshi, the head of the Minamoto clan, who is searching for her under Emperor Shirakawa's order. Maiko eventually gives birth to a baby boy, Heita, who later becomes known as Taira no Kiyomori.

Heita, after reaching adulthood, wanders around gambling parlors being frustrated with his ironic fate of having two fathers: Tadamori as his foster father and the cloistered Emperor Shirakawa as his biological father. People consider Heita to be disreputable, however, Tadamori continues to treat Heita as the heir of the Taira clan, which worsens the relations between Tadamori and his brother, Tadamasa. One day, a fisherman close to Heita is captured by the Emperor Shirakawa for breaking the law that prohibits killing animals set by the Emperor.

Heita, renamed as Kiyomori, spends days fighting against pirates in the Seto Inland Sea and restoring stolen food to fisherfolk. Kiyomori, however, is mistaken as a pirate and sent to Kyoto where he is reunited with Tadamori. Although Tadamori tries to place Kiyomori to guard the Imperial Palace, Kiyomori refuses it saying he wants to live his own life. One day, Kiyomori is called to stop by a man named Minamoto no Yoshitomo, the son of Tadamori's longtime foe Tameyoshi, who later becomes Kiyomori's lifelong rival. Yoshitomo challenges Kiyomori on deciding which of the Minamoto clan and the Taira clan is superior to the other by comparing their horseback riding skills.

Tadamori becomes the first samurai granted a title which allows him to enter the Imperial Palace in recognition of his loyalty to the Imperial Court, which brings joy to the Taira clan including Kiyomori. However, some aristocrats are not pleased with Tadamori's promotion, and Fujiwara no Tadazane from a prominent family in the Imperial Court, plots to make a sneak attack on Tadamori by maneuvering Tameyoshi.

In 1135 at the Imperial Court, aristocrats are discussing countermeasures against pirates who are raising havoc in the Seto Inland Sea. Despite Tadazane's recommendation to place the Minamoto clan to expel the pirates, the retired Emperor Toba, who puts his trust in Tadamori, assigns the Taira clan to lead the punitive expedition. Tadamori, who wants to make Kiyomori his successor, orders Kiyomori to join the expedition, going against the opposition of Tadamasa. After arriving at the Sea, a giant vessel appears before Tadamori and Kiyomori.

Amid the battle against the pirates, Taira no Moriyasu gets seriously hurt from protecting Kiyomori, and the Taira clan once returns to their base. Kiyomori, however, goes back to the Sea alone being mad at his cowardliness, where he is saved from his sinking boat by Takashina no Michinori. Meanwhile, Yoshitomo, who is on his way eastward from Kyoto, encounters Yura Gozen, daughter of the chief priest of Atsuta Shrine. Back at the Imperial Palace, Nariko from a middle-class aristocratic family becomes pregnant with a child of the retired Emperor Toba. Kiyomori and Michinori are captured by the pirates and taken to the giant vessel.

The Taira clan finally succeeds in subduing the pirates, however, Tadamori is not granted the rank equal to the aristocrats. Kiyomori, on the other hand, gets promoted and pays a visit to Tadazane. On the way back home, Kiyomori and Morikuni, fisherman-turned-samurai, encounter Takashina no Motoaki, a lower-class aristocrat, and his daughter, Akiko. Motoaki immediately takes a liking to Kiyomori and asks him to take Akiko as his wife. Although Akiko feels reluctant to marry Kiyomori because of her low status, she gradually falls for Kiyomori as he reveals his honest feelings toward her.

In 1136, Kiyomori learns that Tadamori is illegally trading with Sung and keeps it secret from the Imperial Court. Meanwhile, Fujiwara no Yorinaga, the second son of Tadazane who is known for his all-or-nothing personality, is assigned as the Minister of the Center, which eventually makes the already unstable situation in the Imperial Court worse. Yorinaga finds out about the illegal trading and summons Kiyomori to his place. Kiyomori, however, suggests to Yorinaga for Japan to emulate the prosperous country of Sung, pointing out Japan's wrong political structure.

In 1138, Akiko gave birth to her and Kiyomori's first child—a baby boy. Now, an heir was born to the Heike family heir, and the entire clan rejoiced at the news of this auspicious event.

Tamako (Empress Dowager Taiken), wife of the retired Emperor Toba, gets upset and clutches at Nariko for bringing up unfavorable rumors surrounding Prince Masahito's birth. On that night, Norikiyo, who has a secret crush on Tamako, visits Tamako to comfort her, but becomes beside himself learning of her continued feelings toward the retired Emperor Toba, and unintentionally wrings her neck. The retired Emperor Toba, however, was indifferent and does not blame Norikiyo for this incident.

Emperor Sutoku falls into Nariko's trap and passes the throne to Emperor Konoe, the son of Nariko and the retired Emperor Toba. Meanwhile, Akiko becomes seriously ill and passes away. Seeing Kiyomori frantically pounce on Buddhist priests who were unable to save Akiko, Tadamori feels that Kiyomori has the same fierce temper as his biological father, the late cloistered Emperor Shirakawa.

In 1145, Tamako, who has become a Buddhist nun, is struck down by a serious illness. The retired Emperor Toba loses his composure and orders samurai serving under the Emperor to find narcissus flower to comfort Tamako, which is not normally around in this season. While Kiyomori is looking for the flower, he runs into Yoshitomo who is on the way to deliver the flower to the retired Emperor Toba. Tamako passes away after receiving the flower. Around the same time, Kiyomori remarries Tokiko, his late wife Akiko's apprentice, and Yoshitomo marries Princess Yura.

In 1147, when Kiyomori and the members of the Taira family visit Gion Shrine to pray for the prosperity of the Taira family, they get into a skirmish with armed priests. The incident escalates into a serious political problem, involving the Imperial Court, temples, shrines, and samurai families. While Yorinaga and Michinori (who renamed to Shinzei after entering the Buddhist priesthood) conflict with each other over the treatment of Tadamori and Kiyomori who are under detainment, the retired Emperor Toba decides to talk with Kiyomori directly.

Kiyomori, after being released, faces scolding from his younger brother, Iemori, who flatly says that Kiyomori's behavior was inappropriate as the heir of the Taira family. Yorinaga, who wanted to drive Kiyomori into a corner at the Gion incident, approaches Iemori who was performing a dance at a festival in place of Kiyomori. Meanwhile, Kiyomori bumps into Yoshitomo at a market, and while they are drinking together, they encounter a woman dressed in shabby clothes, named Tokiwa, who later becomes deeply involved with the Taira family and the Minamoto family.

Iemori falls into Yorinaga's trap and dies from falling off his horse, which strongly shakes the Taira family. Tadamori, however, shows no sign of perturbation, and asks the retired Emperor Toba, who had ordered Tadamori to reconstruct the main hall of Mt. Koya, to let Kiyomori lead the reconstruction instead. A year later, Nariko, who has become Empress Dowager Bifuku, hints to Tadamori that he might be granted the title equal to the aristocrats after the completion of the reconstruction. Meanwhile, Yorinaga appears and makes an insulting remark on Iemori to Tadamori.

While the internal power struggle within the Fujiwara family is heating up, Tadamori, who has been promoted after completing the reconstruction of Mt. Koya, is struck down by an illness. Meanwhile, Nariko plots to embroil the Heike family in the power struggle of the Fujiwara family, however, Kiyomori urges Tadamori to reject Nariko's order. Tadamori for the first time tells the members of the Taira family that his purpose of life was to build a samurai-oriented country. After declaring his intention of making Kiyomori the head of the Taira family, Tadamori passes away.

In 1153 after the death of Tadamori, Kiyomori officially becomes the head of the Taira family, however, he starts to doubt his abilities in following the great footsteps of his father. Although the Taira family establishes a new structure after Tadamori's wife, Muneko, became a Buddhist nun, Tokiko is not yet dependable enough to organize household matters, which prompts anxiety among the Taira family. Fujiwara no Ienari, who is concerned about the Taira family, devises a plan to hold a poetry party at the Imperial Court to introduce Kiyomori as the head of the Taira family and make Kiyomori read his poetry there.

In 1154, as the reigning Emperor Konoe's illness worsens, the retired Emperor Toba regrets and wonders if the cause of illness is retribution for him not being in good terms with the former Emperor Sutoku. Kiyomori tries to help mend the relationship between Toba and Sutoku, however, to no avail as Konoe passes away in 1155 at the age of 17. At the Imperial Court, a meeting is held to decide the successor to the throne.

Prince Masahito ascends the throne and becomes Emperor Go-Shirakawa, which throws the Imperial Court into chaos. Meanwhile, a dispute arises among the Minamoto family and the relation between Tameyoshi and Yoshitomo becomes worse. Emperor Go-Shirakawa goes into a frantic rampage after receiving a poem from the former Emperor Sutoku at his enthronement celebration. The retired Emperor Toba, who has fallen ill, hands Kiyomori a hand-copied sutra he wrote for Sutoku expressing apology. Kiyomori goes to deliver the sutra to Sutoku.

In 1156, the former Emperor Sutoku and Yorinaga similarly oppressed, join together. Shinzei puts the two under suspicion of treason and commands the samurais to side to Emperor Go-Shirakawa. While Tameyoshi and Yoshitomo are divided over their decisions, Kiyomori, who had a talk with Emperor Go-Shirakawa alone, tells the members of the Taira family his intention of taking side with Emperor Go-Shirakawa. However, Yorimori, Kiyomori's half brother, hesitates to follow Kiyomori's decision.

On the late night of July 10, 1156, military meetings are held at both sides, the former Emperor Sutoku and the reigning Emperor Go-Shirakawa, where the two forces react differently on whether to launch a night attack on their enemy or not. On July 11, the battle between the two finally breaks out--the Hogen Rebellion. The battle is not simply a dispute over the Imperial succession, it is also the outbreak of interfamilial conflicts of the Fujiwara, Minamoto and Taira families.

The Hogen Rebellion finally comes to an end with the victory of the Emperor Go-Shirakawa side. Yorinaga, who is seriously hurt while escaping, seeks help from his father but the cry for help goes unanswered and Yorinaga passes away. Tadamasa and Tameyoshi, who were defeated in the Hogen Rebellion fighting against Kiyomori and Yoshitomo, are captured and brought back to Kiyomori and Yoshitomo. Kiyomori asks Tadamasa to work together again for the Taira family, however, Shinzei gives a shocking order to Kiyomori and Yoshitomo.

Kiyomori and Yoshitomo are respectively ordered to cut off Tadamasa and Tameyoshi's heads by Shinzei who has now come to power in the Imperial Court. Although the two are torn between sorrow and duty, they finally make up their heart-rending decisions. After following Shinzei's order, Kiyomori is invited by Emperor Go-Shirakawa to his banquet where Go-Shirakawa tests Kiyomori's loyalty to him. Shinzei tells Kiyomori to bear all the burdens and become the country's valuable asset.

Shinzei, who is actively engaged in political events, sends Kiyomori to Chinzei to raise money by collecting unpaid taxes. Meanwhile, Shigemori, Kiyomori's eldest son, not accepting Kiyomori following Shinzei--the person who ordered Kiyomori to kill his uncle, is reluctant with the marriage arranged by Kiyomori. After successfully fulfilling his duty in Chinzei, Kiyomori devises a plan to improve his status by using a tea set he obtained there.

Yoshitomo feels chagrined at remaining in his low status, while Kiyomori is climbing up the ladder of success. Yoritomo, Yoshitomo's eldest son, meets Kiyomori for the first time and gets overwhelmed by his strong presence. Meanwhile, Fujiwara no Nobuyori, Emperor Go-Shirakawa's aide, holds Shinzei in check as he is gaining in power. As Yura's illness worsens, Yoshitomo tries to obtain medicine from Kiyomori, however, Yura tells Yoshitomo to never bow his head to the Taira family and passes away. While Yoshitomo is struck with deep grief from losing Yura, Nobuyori approaches Yoshitomo with plan to eliminate Shinzei.