Ryōsuke Yoshii, an ordinary reseller, carelessly earns grudges by people and becomes entangled in a life-threatening struggle.

Two men, tired from work, visit the town of Chichibu to enjoy their favorite hobby - exploring caves. But little do they know, the town has been secretly protected by the descendants of the righteous Shinobi ninja since the Sengoku period. The two unlucky friends accidentally break a spell that awakens two colossal beasts, Jaron and Goura. The area’s rival clans manipulate them into a fierce battle, bringing chaos to the area. But a righteous female ninja steps up, wanting to stop the destruction and restore the seal. Can she defeat the evil ninjas that stand in her way before Chichibu is completely destroyed by two kaiju?

In the Edo period, at the remote village of Okitsu, the evil cult leader Koushirou uses ninjutsu to bewitch sharks and forces them to attack local pearl divers so the cult can steal the pearls from their mangled corpses. Desperate for help, the village chief hires Kotaro Shiozaki, a guard at a nearby temple, but Kotaro soon finds his path blocked by lady ninja Kikuma and a gigantic shark that doesn't seem like something from this world.

In 1701, Lord Takuminokami Asano has a feud with Lord Kira and he tries to kill Kira in the corridors of the Shogun's palace. The Shogun sentences Lord Asano to commit suppuku and deprives the palace and lands from his clan, but does not punish Lord Kira. Lord Asano's vassals leave the land and his samurais become ronin and want to seek revenge against the dishonor of their Lord. But their leader Kuranosuke Oishi asks the Shogun to restore the Asano clan with his brother Daigaku Asano. One year later, the Shogun refuses his request and Oishi and forty-six ronin revenge their Lord.

Keisuke, a 10-year-old boy, living hard despite being abused by his father, finds a ray of light in the midst of his suffering and conflict ---- a shogi world where he fights quietly and passionately in his sharpened senses. Even though he gives up and tries to escape from the light, his passion for shogi continues to guide him thereafter. Eventually, he would learn the true meaning of life.

Humanity finally rids themselves of Godzilla, imprisoning him in an icy tomb in the South Pole. All is peaceful until various monsters emerge to lay waste to Earth's cities. Overwhelmed, humanity is seemingly saved by a race of benevolent aliens known as Xiliens. But not all is what it seems with these bizarre visitors. If humanity wishes to survive, they must reluctantly resurrect their most hated enemy, Godzilla.

Godzilla has become a distant memory for Japan when the destruction of a US submarine raises alarms for Admiral Tachibana. His estranged daughter Yuri investigates the legend of the guardian monsters, who must rise to protect Japan against the vengeful spirits within Godzilla that seek to destroy both the nation and its people for the suffering they inflicted in the Pacific conflict.