Kamen Rider Agito was basically a long complex story where the real enemy is fate itself (think Timeranger). The Lords as antagonists were killing people with the Agito seed because it was going to be a threat to humanity itself. But B.S. Man is a different story. Unlike Shouichi/Tetsuya in Agito he is not after the good of humanity or trying to solve the conflict of the Lords and humans. Instead, he gets gifted with the power similar to Agito which he misuses hoping to destroy Universal Karma from punishing his friends and allies.
B.S. Man's mythology takes back to the long, long ago when the three Overlords created humanity. These three Overlords once worked in perfect harmony as the Overlord of Creation, Overlord of Preservation and the Overlord of Destruction - all acted by Rei Haneo who played as the two Overlords in Agito.
Once upon a time, the world was chaos and there were three Overlords all acted by Rei Haneo. One was the Overlord of Creation, the Overlord of Preservation and the Overlord of Destruction. The three Overlords lived in harmony. The three of them began the creation of mankind with the help of the other Lords. The three were known as Universal Karma to preserve humankind. As Creation creates then Preservation must preserve and Destruction must destroy. But one huge misunderstanding was about take place.
One day both Preservation and Destruction had a petty quarrel. Not only did Preservation give the gift of fire to man but also the gift of Agito. Destruction thought humans should never hold the power of Agito realizing the dangerous potential it could give them. It was the forbidden power that shouldn't be. During their argument, Preservation accidentally spilled the container containing the Agito seeds which would soon manifest for generations to come. This gave a warning that one born with the BS Agito seed would be born to become the "hero" BS Man and oppose them.
The job of the Lords was to make sure mankind was in good check and balance. Destruction originally wanted to destroy much of man who had the Agito Seed but Preservation taught certain people to use the Agito seed for good. Some of these people who held Agito's power and used it for good were people like Momotaro and Kintaro. Others would use this power for evil and had to be destroyed. The Lords were trying to preserve balance while trying to prevent the rise of BS Man.
The Universal Karma trio agreed to let the Lords punish only those who deserve it either through direct or indirect means. For many years, mankind hasn't been aware that the Lords scheduled karma for all who had been misbehaving. While some Agito humans brought peace and unity but one special evil was about to be born from it. Destruction held Preservation responsible for this incident.
The story also links to B.S. Man's ancestors the Nobinos who are greedy power grabbers. In the dawn of civilization the Nobinos were always up to no good and B.S. Man and his allies happen to be the 13th generation where the Universal Karma may hit them the hardest as they continue in the wayward path of their family. It's also revealed that one generation that one of the Nobino patriarchs took part in the atrocities of the now deceased Empire of Japan during the second World War. Nobita would be born as the special child bearing the power to become BS Man.
In present day Japan, Nobita becomes the ever-dull prime minister but a new "crisis" emerges. The three Overlords send their agents called the Lords (not the same Lords from Agito) to avenge the 13 generations of mistreated farmers in Shibuya. The Lords start attacking B.S. Man's friends and family with repeated karmic actions. B.S. Man who was born as the "chosen child" of the Nobino clan. It's revealed that long ago the three Overlords argued over the evolution of humanity. While Creation and Destruction didn't want to spread the Agito seed (not the same Agito seed of the same show) but Preservation did it anyway causing the other two Overlords to facepalm for a thousand years. Preservation would later regret doing so when generations later B.S. Man would be born with that power. Years later, both Creation and Destruction would leave the Agito seed be unless they were misused and abused but still blame Preservation for what he did. Nobita could only stay in power because the parliament fears his Agito powers which he misuses to entertain himself like the Gorma Emperor in Dairanger.
The finale would be an extreme comedy. The three Overlords begin their plan to destroy the Nobinos' wickedness once and for all to maintain balance in humanity. B.S. Man and his allies try to stop the three Overlords by simultaneously using their Agito powers. B.S. Man tries to "Rider Kick" the Overlords only for it to backfire. The result ends up with them getting spiraled into Universal Karma's inevitable results. After a huge time jump the true villains of the show are revealed to have been reincarnated into different forms depending on how they lived.