Kagami was later chosen by the TheBee Zecter to become Kamen Rider TheBee after it rejected the previous user. Kagami gave up his role as TheBee after he was torn between the orders of ZECT to eliminate Kabuto. He later realized that Tendou didn't want to friends—after accepting this fact and renewing his pledge to destroy all Worms, Tendou let him back into his life. He was later framed by Shun Kageyama as being a traitor to ZECT, but this was simply to lure the real traitor out. He would have died if Tendou had not saved him. When Kagami goes to rescue a young boy, whom he met in the warehouse, the boy is revealed to be Tarantes Worm. Tarantes Worm kills Kagami. After the Worm leaves, a mystery man appears and equips Kagami with a Zecter belt, reviving him with it. Later, Kagami goes on to fight the Tarantes Worm only to be saved by him in the end by shielding him from the explosion detonated by the Shadow Troopers. This convinces him that Worms have a humane side to them, but is mocked by Kabuto.
After seeing Tsurugi's devotion to avenge his sister, Kagami decided to protect Tsurugi. This eventually caused a fight between Gatack and Kabuto to prevent Kabuto from killing Tsurugi. After this, Kagami and Tendou witnessed the transformation of Hiyori to a Worm. Despite her being a Worm, Kagami works together with Tendou to protect her. Hiyori disappears with the man in the iron mask and Kagami does not believe in Tendou's method of collecting all the Zecters so he can save Hiyori. This leads to fight between Gatack and Kabuto, which Gatack ends up losing. Tendou wants the Gatack Zecter but Kagami refuses, stating that Riders are meant to protect humans. Kagami is seemingly destroyed by Cammarus Worm, but he is saved when Hyper Kabuto reverses the flow of time and save his life. Even after this, Tendou told Kagami that they will fight one day to finish things. Kagami is told by the ZECT HQ to protect Daigo Tachikawa at first, but Kagami soon discovers Daigo is not a Worm that destroys humans. Kagami later takes Daigo to Tsurugi's house to heal him.
Daigo realizes Tsurugi is a Worm and uses the Sasword Zecter to escape from him. Kagami was referred to by Tachikawa as Kagami Arata, the one who is chosen by the god of battle. During the battle with Cochlea Worm, Kabuto's Red Shoes System activates, which leaves Gatack alone to try and stop him. Ultimately succeeding, they are attacked by the Hopper Riders shortly after and are defeated horribly. In the end however, Kagami and Tendou make a promise with each other, if Tendou goes berserk again and tries to kill Hiyori, Kagami will kill him, vice versa. Tendou also no longer wants to own the Gatack Zecter, for no one would be able to stop him if Kagami were to ever disappear. When they are attacked by Pupa Worms, the Natives attempt to escape, referring to Gatack as "The Top's son". Confused, he is the first one to meet Reiji Nogi, the executive class Worm that was able to defeat him in one attack. Kagami then goes to his father, and he tells him the origin of ZECT. His father tells him that his soul now belongs to the Native, and Kagami needs to be the one to carry it on.
After hearing this, Kagami begins to fear that his sole existence is to be the catalyst for defeating Worms. His faith is further shattered when he discovers Tadakoro is a Native. He is unable to fight and is defeated by both Pupa Worms and Nogi. Kagami is eventually led off by Misaki, but he is still angry at Tadakoro for hiding the fact that he is a Native. He is chosen as the negotiator to rescue the Natives. Nogi has demanded that ZECT give up their last AMB and they will release the Natives, along with Tadakoro. He even gives up his Gatack Buckle because he is still angry at ZECT. However, after Tendou talks to him, he realizes that his dad wanted him to save the Natives, but at the time keeping the AMB. Realizing that he needs to catch his father's feelings, Kagami takes the AMB from Mishima. They are able to rescue the Natives and protect the AMB, although Kagami is once again defeated by Nogi.
While playing again at the baseball field, he meets his father again, who shows that he does indeed love Kagami and plays catch with him. It is later discovered that Gladius and his Worm army are planning to assault Area Z, the place where the original Masked Rider System was created. After Tendou leaves for Hiyori's world, he meets Kageyama who has once again become TheBee, but their attacks fail, and Nogi defeats them once more. Tendou is able to return to the battle before Tadokoro detonated Area Z. Gatack, Kick Hopper, and Kabuto then execute a three-way Rider Kick, effectively neutralizing Cassis Worm who was then destroyed by Hyper Kabuto. Gatack fight the Worms that are constantly appearing, but he is sidetracked after discovering that Misaki has agreed to Tsurugi's request for a date. Unwilling to tell her that Tsurugi is a Worm, he follows them on their date, only to discover that Tsurugi does indeed lose control, forcing him to save Misaki.
Both Tsurugi and Misaki end up being mad at Kagami. He finally tells Tendou of Tsurugi true identity later, but still believes that he isn't entirely evil. Kagami, unwilling to fight his friend Tsurugi, gets defeated. Meeting Tsurugi again, Kagami tries to convince him to live as a human again, handing him Misaki's present. However, Tsurugi punches him out instead, and takes the Gatack Zecter. Kidnapping him, Tsurugi attempts to destroy all the Zecters, but fails as Kagami and Tendou are able to regain their Zecters. Kagami's dad Riku has finally announced to the world, saying that the Worm threat is finally over. Kagami is given the task of delivering the necklaces that can warn humans when a Worm is near. However, he meets conflict in Tendou when Tendou states that there the necklaces make them into Natives, which Kagami refuses to believe
This leaves Kagami, Todokoro, and Misaki even more furious at Tendou for his unexplainable actions. With the help of the ZECT Troopers, Kabuto is defeated. After defeating Kabuto, Kagami receives a call from Misaki, telling him that Mishima has taken over ZECT. Kagami then goes to rescue his father, who tells him that no matter what, he must believe Kabuto and fight alongside him. During the final stage, Kagami finally realizes that the necklaces, along with Mishima's broadcast signals, are changing humans into Natives. Kagami confronted Mishima and Negishi, only to be defeated by Mishima and is almost killed, until Tendou arrives on the scene. Together with Hyper Kabuto, they are able to destroy Mishima. Within his last moments, Mishima collides with the meteorite, setting off an explosion and ruining their entire operation. After realizing the battle is over, he removes the Gatack Zecter, and letting it go, watches it fly away with the Kabuto Zecter. During the epilogue, it is shown that Kagami now lives as a police man, with his father still watching over him.