Keita Ibuki is currently a high school student living alone in Tokyo while being assisted by his father who remits money for his allowance and daily visits by his old childhood friend, Akane Sano after his mother dies from an encounter with her own doppelgänger as a young boy. After seeing the splitting image of someone with the same looks as his own mother, Keita visits a ramen stall when Kuro shows up with her dog, Punipuni. After Kuro receives her ramen from Keita, she is severely attacked by an unknown assailant who was ordered to capture Kuro alive at all costs despite Keita trying to stop him. He later meets with one of his neighbors, a young girl named Mayu, only to watch a speeding truck run her over after she claims that she had met her double.
Keita and Kuro encounters a Tribal End sent to capture her alive after the previous encounter at the ramen stand was deemed to be a failure due to the Tribal End's defeat at Kuro's hands. In the midst of the fighting, Keita is killed when his heart was pierced by the Tribal End's mysterious Exceed energy in an attempt to fight Kuro. To save Keita before he dies from his fatal wounds, Kuro decides to create a pact between them by exchanging their hearts after she was able to bring him to safety. Kuro was once more able to defeat the Tribal End by electrocuting him after she created the pact with Keita successfully.
Keita had some new issues with Kuro, regarding the concept of Synchronization as he felt his entire life had changed after Kuro created the pact. It was until the encounter with Keita's teacher and covert Tribal End agent, Tsubota-sensei, that Keita realizes that Kuro was right all along and thus teamed up with her to defeat him after Tsubota initially gains the upper hand against Kuro due to issues of synchronizing properly with Keita. The two escape from school, leaving an unconscious Tsubota behind after Kuro was able to incapacitate him by sychronizing together in order for Kuro to use her Exceed abilities against her opponent.
Excel and Steiner conduct a covert mission to test Akane if she has strong Tera energy flowing throughout her body after the two had arrived in Japan. Later on, Akane meets with Keita and Kuro in a small restaurant after being followed secretly by Steiner and Excel from the local bank where she works as a teller. However, the three are ambushed by Tribal End bikers sent to apprehend Kuro and eliminate Kuro and Akane. With Steiner's intervention, he engages Kuro in a fighting match to test their fighting strength after driving the Tribal End bikers away from them when Kuro was not able to defeat the bikers herself.
Steiner faces off against Kuro in a one-on-one match, to the point where the two Tera Guardians were able to show off their Exceed skills and place the match evenly before Steiner was able to subdue Kuro for the count due to his superior skills against her. Despite Kuro and Keita's defeat by Steiner, Excel offers to bring them home with Akane. The two Noble One operatives disclose information regarding the death of Keita's mother when they show a photo of her supposedly in a covert operation conducted in Okinawa under Hiyou's command, bringing Keita bad memories regarding the death of his mother years ago as a child.
Keita is kidnapped from the streets of Tokyo by Mikami Houjo after getting her orders from Hiyou in order to get Kuro to her. Once at the mansion, the two Tera Guardians challenge each other to a fistfight. Both use their Exceed moves in order to overpower each other and gain an advantage, but Mikami loses the match when her contractee Shingo collapses and dies due to health complications when he became very old despite his difference with his age and looks from his time with Mikami in using his contact powers. Seeing that he had die, Mikami no longer wishes to fight them and allows them to leave the mansion grounds for good.
Kuro encounters Yakumo, the ex-ward of Reishin before he massacred most of his tribal clan, in the streets of Tokyo with his new contractee named Riona. Kuro tells Keita how she came to Earth, revealing her origins as the princess of his tribe and the tragic history of her tribesmen after Reishin was told by her mother that he could alter the destiny of the world to either lead it to prosperity or lead it to its doom. Hiyou appears at the airport and fights Kuro before he decides to retreat. Excel and Steiner see Keita and the others at the airport before she gives him the Hex Ring as a gift to help him fight alongside Kuro.
Kuro, Keita and Akane head to Okinawa, staying with Keita's grandfather in order to confirm whether Keita's mother had really died when he was young or not and what to investigate in the island. Reishin had started plans to gather all Master Roots under the protection of the Kaionji Group, led with the assistance of Kuraki. As the trio continue to enjoy their Okinawa vacation, Hiyou and his contractee arrive in Okinawa as well, preparing for another mission.
Steiner and Excel leads a group of Noble One members in raiding the Kaionji Group's main headquarters in Tokyo, only for Reishin to flee to safety after engaging Steiner in combat. Kuro trains in martial arts under Keita's grandfather in order to improve her skills. Keita, by chance, encounters his mother's double before she attempts to steal his Tera energy. While Keita defeats her, Kuro is kidnapped outside the resident of Keita's grandfather by Hiyou himself after attacking Makana.
Keita heads off to rescue Kuro, held as a prisoner by Hiyou while Makane runs off to rescue Kakuma as he was held hostage by Reishin. Shinobu, however, survived the attack by Keita back at the beach and tries to drain off his Tera energy while telling him that she was responsible for killing Keita's mother due to her miserable life under the Doppleiner system before and after making a contract wit Hiyou. After Kuro and Keita were able to synchronize and defeat Hiyou, Shinobu dies as she was not able to tap into Keita's Tera to make herself stronger. When the two leave the cave with Shinobu's body, Keita encounters Daichi who he knows as Sawamura before he collapses due to coughing up blood.
Keita, Kuro and Akane were hidden in Daichi's cottage, revealing that he was supposedly trying to undermine the Kaionji Group and the Shishigami Clan when he told him that his real name as Sawamura, who was supposedly dead when he had jumped in front of a train. He also told him that he wishes to defeat the clan due to their totalitarian dreams of making the Earth fit for Tera Guardians to rule. Kuro voiced her objections to Daichi's plans, saying the Doppleliner system is not a weapon to be used. Meanwhile, Kakuma was killed by a Tera Guardian to gain access to the Tera Stone.
Kuro, Yakumo and Riona escape to ensure Keita's safety while Excel and Steiner engage Reishin in battle with Kaionji Group bodyguards ambushing the escapees on their way out of the cave where the Tera Stone was hidden. Excel was made unconscious with Steiner being unable to defeat him as Reishin plans to use the Tera Stone to begin his plans to conduct genocide. Daichi appears with his Tera Guardian named Raiga and ambush Reishin while he was still using the Tera Stone with the Exceed called the Shidin Sword. Raiga reveals that he killed Kakuma to access the Pure Land. Reishin was then sucked into a wormhole following his defeat with its shockwave reaching mainland Okinawa.
Kuraki begins his plans to establish his own brand of utopia through the whole world as the Kaionji Group's influence reach out even to the Noble Ones, "forcing" them to leave Japanese soil for good. A few Noble One agents remained in Japan, disobeying orders, alongside Yakumo and Kuro to protect Keita as he was still unconscious and to defeat the company by themselves without any help. Pro-Kaionji Tera Guardians raided the Noble One compound in an attempt to capture Kuro and Keita alive. However, Keita unleashes his full potential with Kuro to defeat the attempted infiltration of the compound.
Kuraki was officially to be engaged to Yuki after Reishin's disappearance, to the disgust of most of the Kaionji children. Meanwhile, Keita remains in hiding in the flooded portions of Okinawa via building ruins to avoid detection by Kaoiji Group intelligence despite his wish to save Akane from Kuraki. Bernhard leds a group of Noble One operatives alongside Yakumo and Riona to infiltrate the Kaionji Group Hotel to rescue Akane while Keita and Kuro personally confront Kuraki during a ceremony at the ballroom. In the confusion, Yuki confronts Akane with a pistol and tells her that she must be killed to end her misery as a substitute.
While Kuraki manages to disarm Yuki and prevent her from shooting Akane, Kuro and Keita were able to meet up with an injured Yakumo after his previous encounter with an unknown Tera Guardian. Kuro finds out that the new enemy was Shinra, another one of Reishin's followers before he went renegade after he massacred the entire tribe and went to be recruited by Kuraki. In the fight by Kuro and Shinra, she was able to destroy the ceiling above Akane's room. Keita, Kuro and Akane try to escape with Yuki in tow, but Raiga appears and attacks them. Kuro and Keita assist Yakumo while Yuki and Akane evacuate by helicopter before it began to malfunction while in the air. Kuraki confronts Keita with Raiga and surprised him when he showed him his Master Root.
Kuro faces off against Shinra and Raiga, defeating the former due to a surge of Tera from Keita. Later on, Raiga faces Kuro and was appearing to win thanks to the strength of his Exceed. Keita collapses from exhaustion due to overuse of his Tera, but dual synchronization seals appeared on both of his hands that enabled Kuro to defeat Raiga. As Keita and Kuro celebrated their victory with the Kaionji Group hotel secured by Bernhard, the Pure Land island appears near Japan. With its appearance, a majority of people who didn't have contracts with Tera Guardians collapsed all over the world leading to chaos with a near collapse in society. Reishin appears on the Pure Land, his appearance based on his pre-Earth days.
Kuro and Keita arrive at the Pure Land alongside Yakumo and Riona after being warned by Bernhard to stay off when they found out the people who had fainted are in the state due to the absence of a Tera Guardian. The four confront Aragi and Sora, a team consisting of a human and a Tera Guardian under a Synchornization contract. The two clash with Kuro and Keita, hoping to keep them away from the Pure Land at all costs. Meanwhile, Bernhard and some of the surviving German High Council Tera Guardians had encountered Reishin in another part of the Pure Land. Even with superior numbers, Reishin was able to defeat most of them with the exception of Jean. Meanwhile, Kuro and Keita were able to defeat Aragi thanks to Kuro's Exceed skill.
Mikami Hojo has previously agreed to form a Contract with Excel for hire. Keita goes with Kuro, who senses two Tera Guardians deep within the forest. Meanwhile, Nam is able to heal Yakumo by altering his flow of Tera Energy. Keita and Kuro is having to deal with the two unknown Tera Guardians, later being able to defeat them. Encountering Reishin, Excel and Mikami recall of the deaths of Steiner and Shingo, their respective former Contractees. The two engage in battle against Reishin, soon being able to absorb his Tera Energy. However, as Mikami attempts to give the final blow, Reishin causes an explosion, leading to her defeat.
Keita and Kuro are now on deep pursuit of Kuro's brother. Keita cannot believe what he has just seen... Akane is alive and has formed a pact with Reishin. As the battle continues on, Keita and Kuro feel stronger than ever, but Reishin and Akane's Terra is growing by the second. Keita and Kuro strive to defeat them both and to find out what has caused Akane to join Reishin. Despite their efforts, they are defeated by Reishin and become unconscious while appearing dead.
Reishin and Akane enter a shrine which contains the Masagami, to which Reishin begins to absorb the power of the Master Tera Stone before destroying it. Ghosts filled with dark auras emerge as some begin to scatter throughout the forest, in which Yakumo and Riona synchronize to fend them off. As Keita regains consciousness, it is revealed in the past that Kuro was to be sacrificed to the Master Tera Stone to prevent the rage of the Masagami. However, Reishin, having been against the matter, was forced to slaughter his tribe. Therefore, he had chosen to form a Contract with Akane to break the curse of the Masagami once and for all. As Kuro awakens from her stasis, a surge of Tera Energy is released, soon unveiling that she is the source of the Masagami.
The Pure Place is enshrouded with flames and with bitter cold as the battle between Reishin and the Masagami begins. Kuro awakens from her stasis soon after Keita does, and is shortly suppressed of her inner Masagami. She and Keita now know that Reishin was not the one to really slaughter his own clan and has done all he has done up to this point in order to protect Kuro from awakening as one of the Masagami and contributing to the destruction of the world. Reishin is pounded by attacks of magma and glaciers, but with the aid of the Thousand Iolite Abyss, he unleashes the powered-up Exceed Tera Cannon to destroy the body of the two Masagami. With his last-founded attack, he uses up all his Tera and dies while impeding the Masagami's ability to regenerate.
Armed with the power of the Masagami, Keita and Kuro synchronize and head into battle. The Masagami, having lost the ability to regenerate after being hit with Reishin's Exceed, merge their bodies into one to escape death and attain a new power. They battle Kuro, but ultimately are finally destroyed when Keita and Akane combine their Tera to give Kuro an ultimate exceed. Life begins to return to normal and Keita discovers that the Doppeliner system has not been stopped. Kuro, blaming herself for the Masagami's curse, decides to isolate herself from the human world and live in the Holy Land for eternity to put an end to the curse. Kuro bids a tearful farewell to Keita and leaves to return to the Holy Land. On the way to the Holy Land alone, she cries while professing her love for Keita; she says that she will not be able to see him again. As she does, Keita contacts and bonds with her through Syncro and she cheers up.
A recap of events that occurred between episodes one through twenty two, mostly from Kuro's point-of-view. In the present, after the destruction of the doppeliner system, Akane is getting married to Keita, and thanks Kuro for allowing them to reach that point. Several decades later, Kuro receives a telepathic message from a very old Keita, despite isolating herself in the Holy Land. Keita tells Kuro that he will be taking "their curse" with him, and thanks her for everything she did for him and that he lived a life of happiness. After delivering his message, Keita dies just before his grandchildren come to get him for dinner. Relieved that Keita was truly happy, Kuro cries and tells her beloved contractee to rest in peace.