Seemingly an average man, Joe Logan leads a peaceful life in the countryside with his wife and child. However, the Logan family have actually assumed false identities to escape from Joe's past as a fearsome ninja assassin. Despite a string of high-profile murders of his former peers, Joe is sure that his new life is secure—but his tranquil bliss is soon shattered when his family is slaughtered by members of his former clan. Left for dead, Joe wakes up in a hospital, unsure of how he survived the wounds that should have killed him. Police detectives Emma Samanda and Mike Moriss, assigned to investigate the Logan family's deaths, witness another attempt on Joe's life. However, this time Joe is prepared. Unleashing secret techniques, he easily dispatches his enemies, shedding his new identity in the process. Embracing his old ways, Joe shrouds himself in his former persona, cutting through the organization he once served in the name of cold-blooded revenge. Assisted in his hunt by the detective duo, Joe will stop at nothing to kill his past and the demons hailing from it.

On the 20th floor of the Tower, the "Regulars" who have been permitted to enter have to undertake arduous and extremely expensive tests to rank up. Most abandon hope and choose to stay where they are—but not Ja Wangnan. Wangnan is determined to reach the top and become the king of the Tower. However, he is weak and has repeatedly failed the exam, with debt collectors tailing him. In desperation, he attempts the exam one more time, only to encounter a mysterious and powerful individual: Jyu Viole Grace, a member of the crime syndicate FUG. Cursing his rotten luck, Wangnan has no choice but to form alliances with strong people, including Viole—who still refuses to be part of any team. Amid a dire situation, Wangnan must find a way to change Viole's mind to finally advance past the 20th floor, or he will never get a chance to build his legacy.

There is a tower that summons chosen people called "Regulars" with the promise of granting their deepest desires. Whether it be wealth, fame, authority, or something that surpasses them all—everything awaits those who reach the top. Twenty-Fifth Bam is a boy who had only known a dark cave, a dirty cloth, and an unreachable light his entire life. So when a girl named Rachel came to him through the light, his entire world changed. Becoming close friends with Rachel, he learned various things about the outside world from her. But when Rachel says she must leave him to climb the Tower, his world shatters around him. Vowing to follow after her no matter what it takes, he sets his sight on the tower, and a miracle occurs. Thus begins the journey of Bam, a young boy who was not chosen by the Tower but opened its gates by himself. They call his kind "Irregulars"—beings that have shaken the very foundation of the Tower each time they set foot inside it.

Second part of Tower of God Season 2.