The setting is Shibiru City, Yukimachi Town. While most citizens are enjoying the peace and quiet, one young man makes a stand. His name is Hazama Masayoshi.

Shibiru City is now home to a superhero named Samurai Flamenco. By pure chance, policeman Goto Hidenori learns the identity of Samurai Flamenco, resulting in numerous headaches as he copes with the new hero's atypical sense of justice. Goto arranges for a meeting to put a stop to all of the trouble, but Masayoshi shows up drenched. Masayoshi explains that he doesn't use umbrellas because of an incident in his past.

Samurai Flamenco is receiving more and more views on video sharing sites. Masayoshi is very pleased until a news site begins offering a reward to the person who unmasks Flamenco. That is when another person comes out as Samurai Flamenco. Who is this fake and what is his objective? The battle of Samurai Flamencos is about to begin.

After dealing with the imposter, Samurai Flamenco gets to catch his breath, but then he's captured by some lawbreakers he approached. When all hope appears to be lost, a mysterious new hero appears and saves him. However, the new hero knows Samurai Flamenco's true identity and sees him as a rival. Samurai Flamenco now has a rival superhero. What next?

Samurai Flamenco is becoming jaded as Flamenco Girl runs him ragged. The police have been receiving an increasing number of complaints as the heroes wreak havoc. Masayoshi struggles with his work as it seems that nothing is going right. Masayoshi begins to wonder what it means to be a hero.

A huge sum is offered to whoever exposes the identity of Samurai Flamenco and Masayoshi is facing the risk of his secret identity exposed, until scientist Jun Harazuka appears with some weapons disguised as stationary to help him.

The efforts of Samurai Flamenco and the Flamenco Girls bear fruit and the city becomes a safer place, but Masayoshi is devastated upon learning the secret behind his parents' death. When doing a PR event with the police, Masayoshi and Hidenori find themselves in a pinch when a real monster appears before them.

King Torture, leader of the evil "Torture" organization declares his intention to enslave the people of Japan and dares Samurai Flamenco to challenge him. Since then a monster attacks the city every week, just to be defeated by Flamenco with assistence from Hidenori and the Flamenco Girls. As the heroes always defeat Torture's monsters, the Japanese Government stops caring about it at all and both Masayoshi and the Mineral Girls have a huge leap in their careers, unaware that according to King Torture, everything is going as he planned.

As the monsters sent by Torture are defeated by Masayoshi without further casualties, the population stop bothering at all for their battles and even Mari stops lending him a hand, determined to confront King Torture himself instead. However, Mari ends up captured by King Torture who uses her as a hostage to challenge Samurai Flamenco for a decisive battle.

Samurai Flamenco and King Torture finally come face to face for their showdown. In the occasion, it is revealed that just like Masayoshi, Torture was a boy who enjoyed superhero stories but once realizing that the heroes he idolized never attain the true peace they fight for, he decided to turn to evil instead. After defeating the villain and stopping his master plan with Hidenori's help, Masayoshi reveals his secret identity to the world.

Just as the press question Masayoshi about his identity, a mysterious floating island rises from the Tokyo Bay. Joji reveals to Masayoshi that this is the work of From Beyond, an alien organisation that provided Torture with the power to make monsters. To this end, Joji has been assembling a team known as the Flamengers, planning on recruiting Masayoshi as their leader. Upon reaching their secret base, however, they discover it has been infiltrated by a toxic commander from From Beyond named Ugly Toxic Poison. Joji assembles four more Flamengers, who are all confused over being allegedly recruited as Red Rangers, asking them to sort amongst themselves who gets to be leader whilst he goes to confront Poison. After Joji's noble 'sacrifice', the group decide to let Masayoshi be the leader and confront Poison, who soon grows to enormous size but is defeated by the Flamengers' Flamen Robo.

As the Flamengers continue to defeat monsters from From Beyond, Masayoshi is still trying to adjust to his role as a team leader. Meanwhile, Mari has been hiding from the public eye at Hidenori's place, feeling she has no place to return to. The Flamengers have a documentary filmed about them as they go against some From Beyond monsters turning cities into an ice age. After defeating two monsters who were holding some kids hostage, they are soon confronted by a large group of monsters, but with some teamwork and new weapons, they overcome them. The team soon act on more friendlier terms with Masayoshi, until they learn there are yet more From Beyond monsters to come.

With From Beyond allegedly sporting over 60,000 monsters at their disposal, Masayoshi finds himself under a lot of stress, particularly when he learns of an all-out attack on Japan being planned for February 7. Joji convinces the Prime Minister to make an announcement, on the condition it be made after the leaders and their families are evacuated first, giving the Flamengers 24 hours to each choose five people to move to the shelters with them. Whilst going to speak with Hidenori, Masayoshi discovers Mari staying with him and is unable to tell him about the evacuation. As Masayoshi finds he cannot limit his choices to just five, Joji tells him his decision to not tell anyone, only to disappear the next morning. Masayoshi, paranoid that an attack could occur at any moment, decides to make his own announcement during a talkshow appearance.

Just as Masayoshi makes his announcement, members from From Beyond call all the cellphones in the area, stating they will attack the next morning. After the prime minister declares a state of emergency, Masayoshi is picked up by Sumi and Akira, who had learned of the government's plans. Feeling responsible, Masayoshi makes his own broadcast to encourage the panicked citizens to be heroes in their own way, allowing them to reach shelters without hassle. The next morning, Hidenori brings Moe and Mizuki to his apartment to talk things out with Mari before heading to his post. As From Beyond's attack begins, they bring forth a 'Destruction of Japan Device', which plots to drill into Mt. Fuji, causing it to erupt. Just as things look their worse, Joji returns, bringing with him various tokutatsu heroes to help the fight, encouraging the citizens to fight alongside them. Just as the Flamengers are about to take on the destruction device, Masayoshi receives a call from From Beyond's final member, who claims to be his brother, Beyond Flamenco.

Beyond Flamenco states a lot of cryptic messages, before taking his own life, causing all the From Beyond members to disappear. With the destruction device still running, the Flamengers try to use all their Flamen Robo's weapons to try and stop it, managing to stop it in time and safely escape. With peace returned to Japan, the Flamengers disband and return to their daily lives. Meanwhile, Masayoshi, still curious about Beyond Flamenco's last words, is approached by an American hero named Mr. Justice, who protects him from the Bureau of Peace who are after him and the other Flamengers for some reason. Justice informs Masayoshi that the Japanese government, led by the prime minister, created From Beyond as a means to distract countries from wars and improve their political standing, just like in his country. As the Flamengers were seen as a threat to the Japanese government's plans, they decided to frame the Flamengers for attempting to overthrow the government. Justice helps Masayoshi escape whilst he himself is apprehended, leaving Masayoshi fleeing as he is put on Japan's Most Wanted list.

Mari, who had ran off from Moe and Mizuki after backlashing at them, revisits King Torture's hideout, reminding herself of the horrors she and Moe went through and lamenting her own worthlessness. Moe and Mizuki catch up to her and the three manage to make up with each other. Meanwhile, Mazayoshi, who is still in hiding from the authorities and growing weak from hunger, meets a short-sighted homeless man who offers him some food. He explains how when life was treating him badly, it was Samurai Flamenco who taught him to help others. Encouraged by his words, Mazayoshi goes to Hidenori, who has been waiting for him to come seek his help.

Masayoshi escapes with Hidenori and Jun, who have been in contact with each other whilst he was in hiding, arriving at a secret base where Akira awaits, later joined by Mr. Justice. The next day, Masayoshi and Hidenori arrive at the Diet to stop Prime Minister Okuzaki from passing an anti-superhero bill. Okuzaki equips himself with a powerful mech suit, powered by support from the public, and starts attacking Masayoshi, overpowering all of his techniques. Whilst Mari and the others hold off Okuzaki's guards, Hidenori joins the fight but is also beaten. However, Akira manages to stream the action, and Okuzaki's plot, on television to the world, rapidly decreasing his support and weakening his suit, allowing Masayoshi and Hidenori to defeat him. However, it is soon revealed that Mr. Justice is actually an Alien Flamenco, whose race had replaced all the world's leaders, which Okuzaki was trying to put a stop to. Stepping outside, Masayoshi and the others are shocked to find a giant spaceship in the sky.

A mysterious being calling himself a Flamencolian appears before Masayoshi and the others, wishing to speak to Masayoshi alone. Despite concerns that he might not make it back alive, Hidenori encourages Masayoshi to go into the Flamencolian's spaceship, where he explains he was the one responsible for King Torture and From Beyond's monsters, believing evolution is the key to universal peace. Unable to persuade him to join their cause, the Flamencolian grows in size to attack Masayoshi, who uses the Flamencolian's evolutionary device to grow in size too, becoming Space Final Flamenco, knocking the Flamencolian into an endless journey into deep space. Stranded on the moon following the battle, Masayoshi is greeted by a being calling itself the universe's will. He explains all of the enemies Masayoshi has faced came because he wished for them, giving him the choice of whether to continue fighting evil, or live on in peace. Masayoshi decides to return to his own world, choosing to keep being a hero not to fight enemies, but to do what is right. After getting to speak with the spirit of his grandfather and learning the somewhat uneventful meaning of "Flamenco", Masayoshi is sent back home where he meets up with Hidenori.

Six months has passed and life has been peaceful for Masayoshi, who people are keen to make World President. Meanwhile, Hidenori makes plans to meet up with his girlfriend for a long-awaited date. Upon hearing about this, Mari drags Masayoshi along with him to follow Hidenori to his hometown. There, Hidenori's mother explains that Hidenori had a girlfriend during high school, who disappeared one day and was never found. She then reveals that Hidenori had in fact been sending texts to himself impersonating the girlfriend in order to keep his sanity. As Mari feels downhearted upon learning about this, she spends the evening with Moe and Mizuki. Meanwhile, Masayoshi encounters a boy named Haiji Sawada, who sets off an explosion in a building.

As Masayoshi is left with many questions about Haiji, he receives a call from him whilst staying in a hotel, explaining how he became obsessed with him after witnessing his earliest superhero efforts, deciding he wanted to become his arch nemesis dedicated to doing bad things to Samurai Flamenco. Masayoshi becomes further confused when he hears from the police that Haiji Sawada allegedly died from illness one year ago. The next day, after Haiji tells Masayoshi he intends to do something 'colorful', malicious things are done to the Flamengers, with Jun being pushed down the stairs and Joji being hit by a truck. After receiving more threats from Haiji, Masayoshi meets up with Hidenori, who offers little comfort and even becomes angry when he brings up her missing girlfriend. Upon realising that the only one who has seen or heard Haiji is himself, Masayoshi starts to wonder if he is just imagining him.

After being informed about Haiji, Mari steps up on stage for her concert, only to find Moe and Mizuki had been poisoned. Meanwhile, Masayoshi is called to the hospital by Joji, who had heard someone mention Samurai Flamenco before he was hit by the truck, telling him that he needs to learn to love to become stronger. As Masayoshi becomes hung up over what that means, Sumi offers to give him advice about his situation, asking Akira to investigate Haiji before teaching Masayoshi about the various types of love. Meanwhile, Haiji lures Hidenori into a trap and kidnaps him, instructing Masayoshi to go to his old apartment.

Hidenori recalls how he started sending messages to himself after his girlfriend went missing, despite attempts from his mother to get him to stop, eventually joining the police force in the hopes of one day finding her. Back in the present, Haiji attempts to drive Hidenori into killing him by deleting the texts that have kept him going all this time. After hearing from Akira that Haiji had his parents fake his death, Masayoshi arrives at the apartment to confront Haiji, who desires to turn Samurai Flamenco into a 'dark hero' by having Hidenori kill him. Believing fighting him as Samurai Flamenco won't solve anything, Masayoshi strips naked in order to confront him as himself. As Hidenori tries to aim Haiji's gun at him, Masayoshi stands in his way and manages to calm him down in his own way, whilst Mari apprehends Haiji. Six months later, a museum is opened to celebrate heroes, whilst Masayoshi, who occasionally pays visits to Haiji, continues to act as Samurai Flamenco to help solve the little crimes.