Years after retiring from their formidable ninja lives, a dysfunctional family must return to shadowy missions to counteract a string of looming threats.

The seven secretaries who consist of the "Shadow Army" enjoy peaceful days. They receive a new request from Koichi Ogata, who runs a ramen restaurant in Nagano prefecture. He is furious at land development that is carried out by Alps Raicho Group. The Alps Raicho Group and their Alps Raicho Resort are run by the Tsukumo family. That family exerts tremendous influence around the region. The Tsukumo family seem like a well mannered family, but, in reality, they are a vicious family who will do anything for their own interests.

In 1879, Kenshin and his allies face their strongest enemy yet: his former brother-in-law Enishi Yukishiro and his minions, who've vowed their revenge.

Before he was a protector, Kenshin was a fearsome assassin known as Battosai. But when he meets the gentle Tomoe Yukishiro, his story begins to change.

Kenshin trains with his master to learn the final techniques he needs to stop Shishio from taking down the government and plunging Japan into chaos.