One of the leaders of the Natives, Negishi seems like a fun loving person despite the deep respect ZECT offers to him. When he first meets Tendou, he asks if he can be Tendou's fan. Despite his innocent look, Negishi actually has his own agenda and later carries it out once the Worms had been almost decimated. Believing Natives and humans would be unable to co-exist, Negishi sets up the plan to turn all of humanity into Natives. To that, he placed Mishima as leader of ZECT and disposes Riku Kagami. However, Negishi didn't count on Tendou's words to sway his comrades to have second thoughts of his plan. In the end, Dark Kabuto manages to capture him, dragging him inside the TV studio explosion that kills them off.
Masato Mishima
The aide of ZECT HQ's leader, Riku Kagami. Eventually, he was upset with Yaguruma botching a mission and Tadokoro questioning him about ZECT's agenda. There's implication that he has no faith in Kageyama as TheBee, despite Kageyama being loyal to ZECT and is looked down upon by Kamishiro. He has no sense of taste, and finishes eating by taking a supplement. He forcefully became TheBee at one time despite the TheBee Zecter's attempt to reject him. He truly thinks Kageyama is an eyesore because he can only complain and has lost the TheBee Zecter. He always kept the Hyper Zecter with him. Mishima tries to destroy the Hyper Zecter with the bomb. However, he doesn't realize the power of the Zecter as it manages to finds its way to Tendou. He gradually loses respect for Riku Kagami's servile manner toward the Natives. After realizing Negishi found out about the Red-Shoes system, he makes a pact with Negishi and overthrows Riku Kagami as leader of ZECT. Using the Natives' pendants, he gains the ability to turn into Gryllus Worm, the strongest Native. He is defeated by Hyper Kabuto's and Gatack's Rider Kick and then destroyed by the meteorite explosion that obliterated the studio set.
Shuichi Tadokoro
Misaki and Kagami's direct superior in the field, he is a very stern man who commands numerous amounts of ZECT Trooper platoons. He was seriously injured when he tried to use the Gatack Zecter in order to save Kagami from being chosen. He does care a great deal about his team, especially Kagami and Misaki and will do anything to help them. He has a younger brother who runs the buckwheat-noodle restaurant which was once his father's business. Although he was the better cook, his brother inherited it anyways. After shielding Kagami, his true form is a Native Worm. However, he has no intention of conquering humanity like Negishi. During the epilogue, it is shown that he has taken over the running of the family business.
Riku Kagami
Arata and Ryo's father, Riku Kagami is a high ranked official in ZECT, and serves as a figurehead to hide their connection to the Natives. Arata seems to despise him because of Ryo's disappearance, as well as the lack of concern or activity done in order to find Ryo. Arata is also unaware that his father is even part of the organization, ZECT, let alone the leader. A mysterious person who always quotes animal bibles, he is also the chief of police. He is a highly trained fencer and plays the cello. Tendou later confronted Riku, ended with Riku telling him that Tendou's sister was not in good hands. Later, he displays that he indeed knows about the Hopper Riders, saying they have opened the Gates of Hell. He also says the Rider's grand plan will be completed by our sons, showing that he did indeed know Tendou's father. He tells Kagami of the secrets behind the Masked Rider System. He also tells Tendou that his father was the one who installed the Red Shoes system in the Zecters, and in turn, Tendou decides to trust him. Riku is overthrown from his leadership position at ZECT by Mishima after revealing to Negishi the Red-Shoes system implemented into the Zecters. He is still alive in the epilogue watching his son grow up.
Yuzuki Misaki
23 year-old technician and agent for ZECT, she travels with Kagami in the field tracking the movements of the Worms. Later on, she is given the assignment to track Tendou and the stolen Kabuto Zecter. At first she is a tough as nails but soon she begins to question the actions of ZECT and eventually gains respect for Tendou after he rescues her from the Worms. However, she was still irritated by Tendou when he implies that she and Kagami make a cute couple. She used herself as bait by disguising herself as Phantom Thief Shadow and tended to Kagami when the Gatack Zecter attacked him. She loves buckwheat soba, and can eat entire ramen bowls in seconds. A Worm disguised as her was sent to attack Tendou's sister, but ended up meeting Tsurugi. The Worm reminded Tsurugi of his dead sister, but he ended up destroying the Worm. However, because of this, he gained a strong attraction to Misaki. As the series progressed, Misaki slowly began to reciprocate to Tsurugi's feelings, and accepted his request to spend Christmas day with him. Unfortunately, Tsurugi became aware of the fact he was Scorpio Worm and was eventually destroyed in battle by Kabuto, despite Misaki's pleas to stop. During the epilogue, Misaki becomes the head of Tsurugi's corporation to honor his name.
Renge Takatori
Formerly a Bright Trooper, a trainee of ZECT and Tendou's second in command who was sent by Mishima in order to spy on and assassinate Tendou. However, she yearns for Tendou as a master after she tasted his delicious cooking. Prior to meeting Tendou, she had eaten nothing but dry boiled rice for the last seven years of her life, considering the concept of taste and deliciousness a sin. She booted Kageyama out from the ZECT HQ. Afterwards, Mishima orders her to kill Tendou, but she is persuaded by Tendou to forget Mishima and help him steal the Hyper Zecter. She is eventually knocked over the building by the Uca Worm only to be saved by Tendou. Despite her sweet and innocent demeanor, she is a fearsome fighter armed with a wire which can cut through almost anything. However, she is still relatively weak against Worms, but tries to fight anyway. After accepting Tendou as her superior, she began to work at the Bistro la salle, although she often misinterpreted recipes and created horrible dishes as a result. She was hit by a bullet that ricocheted off Kabuto's Kunai Gun, hitting her in the shoulder. As an apology, Tendou made a meal for her while she was recovering in the hospital, also giving her a letter to Kagami. During the epilogue, Renge continues to work at the Bristo La Salle.
ZECTroopers are foot soldiers of the organization ZECT, they are armed with the Machine Blade Gun and a grenade launcher-like shotgun as a last resort and means of retreating; And flash bombs which disable Worms and seem to prevent them from molting. They are transported to the Worm hotspots via black, white, or silver Humvees. They lack any concern for civilians. The special team known as Shadow assists Kamen Rider TheBee. Unlike regular ZECTroopers, they have yellow pin stripes on their uniforms. Shadow is able to prevent the Worms from molting, enabling TheBee to kill them. During a training mission, the ZECTrooper trainees, Bright Troopers wear white armor instead of the standard black. It's revealed that the majority of ZECTroopers are Native Worms. However, after a speech by Tendou, they turn on Negishi and Mishima, aiding the Riders.
Machine Blade Gun
The ZECTroopers' weapon consists of an automatic machine gun with a retractable blade, which they use for close-quarters combat.
Series:  Kamen Rider Kabuto