Grisaia no Rakuen begins right at the end of the previous installment, Grisaia no Meikyuu. Kazami Yuuji is arrested under suspicion for terrorism. A video showing apparently concrete proof that Yuuji committed these acts, and he is held in custody by Ichigaya. Ichigaya knows full well that Yuuji didn't commit the crimes he has been accused of. But he did fail to assassinate Heath Oslo, who is the leader of the terrorist organization with an extremely devastating weapon in their possession. In fact, Ichigaya have their own plans for Yuuji... But all may not be lost for Yuuji. The girls of the Mihama Academy are not about to let Yuuji be used for political gain, and neither may the mysterious new figure which appears before them.

In a barren frontier where people trade goods with each other in order to help each other survive. The Kotobuki Squadron are bodyguards for hire, led by a strict but beautiful squadron leader, an unreliable commanding officer, and a true artisan of a crew chief. Alongside pilots who don't lack for personality, they take to the air in dogfights, letting the engine noise of their Hayabusa fighters ring out in the skies. (Source: ANN)

In a research facility hidden away on a remote island, genius programmer Shiki Magata has lived as a recluse for years. She rarely sees guests, but associate professor Souhei Saikawa and university student Moe Nishinosono still seek her out. However, their meeting is cut short when they are caught up in a locked-room murder mystery. Everything is not as it seems, and many secrets are hidden. Within an isolated facility, a seemingly impossible and gruesome crime takes place, and Saikawa and Moe must unravel the truth behind the murder and Magata's shrouded past. [Written by MAL Rewrite]

On a planet far from Earth, there is a kingdom full of smiling faces. Princess Yuuki is 12 years old, and about to enter a sensitive age in a person's life. Everyday, she cries, laughs, and sometimes, her heart throbs with excitement. All the while, she lives merrily in the royal palace. Filling her days are her loyal vassals: her tutor Reira, Izana who assists in political affairs, the leader of the chivalry Harold … and then there is her childhood friend and aide Joshua. "Yuuki! If you have spirit and guts, you can do anything!" "…No, not this again! Joshua, be nobler!" Stella is 17 years old and a capable, reserved soldier. However, she is always smiling ... for smiling is essential to living. This is a story of two girls born on distant planets. (Source: ANN)