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.

Reina Aharen, a small and cute student with a quiet voice, is quite bad at determining distance and personal space. Sometimes she's inches away from your face, and at other times, miles too far! The only one who tries to understand her antics is Raidou Matsuboshi, who is seated beside her in class. He has a menacing face, but in reality, he is a kind boy with an imagination that can run wild at times. Aharen-san wa Hakarenai follows the peculiar pair as their odd friendship starts to blossom when Raidou picks up Aharen's eraser for her. She misinterprets his gesture and now believes them to be best friends, showing how the simplest of things can prove to be the most complicated of challenges for them.

Deep in the Ararat Mountains of Turkey, a secret organization known as ARCAM has found what is believed to be Noah's Ark. However, the U.S. Machine Corps., a rogue organization of the Pentagon, wants to take over the Ark as a means of global supremacy. Only a special ARCAM operative known as a Spriggan stands in their way. Japanese Spriggan Yu Ominae teams up with French Spriggan Jean-Jacques Mondo to combat members of the U.S. Machine Corps. led by Col. MacDougall—a genetically-enhanced boy with deadly psionic powers. However, they must act fast and stop MacDougall before he uses the Ark for his own agenda.

Shu is from Datania, a country that makes young children work. He and his friends were trying to escape when they met the Returners. The Returners are some kind of rebels to Datania. Shu goes with the Returners to fight Zero, Nines, and his men who are after DT, a special substance inside humans.