The end of the demon wars has ended and now the Flower Division has been able to rest up after their fighting. The second Sakura Wars developes studies on every Flower Division Combatee in every episode while they go on their miscellanious adventures around Japan.

The Lost Ones are wanderers who come here from a distant world known as "Japan." No one knows how or why they leave their homes. The only thing that is certain is that they bring disaster and calamity. The duty of exterminating them without remorse falls to Menou, a young Executioner. When she meets Akari, it seems like just another job...until she discovers it's impossible to kill this girl! And when Menou begins to search for a way to defeat this immortality, Akari is more than happy to tag along! So begins a journey that will change Menou forever...

Taba and the Girls of Kagura Total Security Inc. specialize in jobs where their enemy are "Phantom Cats". They have a few run ins with the various Government agencies, as well as a gang of Phantom Cats; blowing up a lot of stuff along the way. When one of their own is kidnapped, they have to get her back.

At the beginning of chaos, the world was divided into three realms: the realm of deities, the realm of men, and the realm of demons. The realm of deities sent a spirit seed down into the world to help the common people. But the spirit seed continuously absorbed the evil of the world and cruelly harmed living things. In the end, Sen Luo, the king of the deities, sacrificed himself and sealed it. However, because of it, the Shangqing Xianmen, where the realm of deities is located, gradually waned and was lost in history. A thousand years later, the ruins of Shangqing Xianmen started to appear in succession. All major sects fought their hardest for possession of the treasures in the ruins.