After battling Alien Flamenco and talking to the will of the universe, Masayoshi returns to Earth and finds peace and quiet in a world without evil. There are no bad guys left, so Masayoshi no longer has anything to do as a superhero.

A gunshot rings through the night. Masayoshi races to find Goto who has been captured by Haiji. Masayoshi wanted to be a hero. Goto wanted to hold onto his girlfriend.

After King Torture's death, Samurai Flamenco reveals his identify before the press. But in the next moment, Masayoshi is taken away in a aircraft that appears out of nowhere. At the same time, a giant fortress appears in Tokyo Bay. Out of the frying pan and into the fire. What will happen to Samurai Flamenco next?

The Flamengers become the first citizens of Japan to receive the National Hero award as the country places its hope in them. They are doing well in the battle against From Beyond, but one day, the monsters suddenly vanish. It seems unlikely that they've given up on taking over Japan. The Flamengers believe that an all-out attack may be coming and begin to prepare, but they encounter an unexpected obstacle.

After the press conference, phones begin to ring across Japan. It turns out that the missing monsters of From Beyond are calling to announce their upcoming all-out attack. Little time remains. The Cabinet declares a national emergency and orders the JDF and police into action. After Kaname goes missing, the Flamengers are forced to take lead themselves. From Beyond's attack is about to begin.

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.

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.

Masayoshi's efforts have paid off, as Shibiru City has seen a drop in crime. His acting career is also picking up. Life is looking good, but Masayoshi isn't celebrating. Instead, he begins to question what he should be doing as a hero. Troubled, he returns to reading his grandfather's notebook, but it turns out that the story of Samurai Flamenco hides a shocking secret.

A mysterious figure named King Torture has dispatched monsters across Japan. They demand the unconditional surrender of the Japanese government and the enslavement of the populace.

Kaname turned out to be the commander of Samurai Base, a counter-secret-organization unit. Masayoshi is joined by new allies, Soichi, Hekiru, Anji, and Sakura to form the Flamengers who fight to defeat From Beyond. However, the Flamengers are very different people who struggle to work together. As their leader, Masayoshi grows worried as monsters continue to attack.

The monster that looks exactly like Masayoshi addresses him as Big Brother and calls himself Beyond Flamenco. Masayoshi is visibly upset as Beyond Flamenco begins to speak about From Beyond's purpose and objective. At the same time, it appears that the government also has another trick up its sleeve. How will the battle with From Beyond end?

The government has framed the Flamengers as terrorists who were responsible for the From Beyond attacks. They have also proposed a bill which bans vigilante activities.

Masayoshi's last hope is Goto. Goto gives him a warm welcome, despite the fact that he is a wanted fugitive. However, they immediately find themselves surrounded.

With help from the resurrected Flamenco Girls, Masayoshi is able to defeat the Prime Minister. However, the government's true objective wasn't to defeat the superheroes.

The boy named Sawada Haiji has put an end to the temporary peace. He was one of the middle school students that Masayoshi had lectured as Samurai Flamenco. Haiji declares that he is Masayoshi's last enemy. He then proceeds to attack the Flamengers, Kaname, and other people who are associated with Masayoshi.

Masayoshi thinks about taking his own life to stop Haiji. After multiple incidents and an argument with Goto, Masayoshi runs into another wall as he attempts to track down Haiji. Goto is also in a difficult position. That is when Haiji makes his next move.

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.

The monsters have become part of everyday life. Their attacks are nothing more than a nuisance to the public, leaving Mari wanting more excitement. While the initial excitement has died down, the attention that is still being paid goes to the monsters and Samurai Flamenco. Unhappy, Mari makes an unexpected move. Meanwhile, Harazuka has a theory about the monsters' peculiar behavior.

Samurai Flamenco heads to the enemy base to save Flamenco Diamond. Flamenco Diamond and Flamenco Sapphire are undergoing torture after being captured. Diamond tries to protect Sapphire, but King Torture reveals an inconvenient truth. Finally, Samurai Flamenco faces off against King Torture. The true objective of the Evil Army will come to light!

Flamenco Girl has powered up by recruiting additional Flamenco Girls! She's enjoying life as she fights evil and performs as an idol. Meanwhile, Samurai Flamenco is on the run as the citizens have turned against him.