On November 22, 2010, Japan was hit by missile strikes, a terrorist act that fortunately did not harm anyone, becoming known as Careless Monday. Quickly forgotten, society goes on about their lives as normal. During her graduation trip to America three months later, friendly college student Saki Morimi's life is forever changed when she finds herself saved from unexpected trouble by Akira Takizawa. Takizawa is cheerful, but odd in many ways—he is stark naked and suffers from amnesia, believing himself to be a terrorist. In addition, he possesses a strange cell phone loaded with 8.2 billion yen in digital cash. Despite Takizawa's suspicious traits, Saki quickly befriends the enigmatic young man. However, unbeknownst to her, this is the beginning of a thrilling death game involving money, cell phones, and the salvation of the world. Higashi no Eden chronicles Saki's struggle to unravel the mysteries behind her savior, while Takizawa himself battles other individuals armed with similar cell phones and returning memories which reveal his possible connection to the event from months ago.

The number of terrorist acts in Japan has never been lower, thanks to the efforts of a syndicate called Direct Attack (DA). The organization raises orphaned girls as killers to carry out assassinations under their Lycoris program. Takina Inoue is an exceptional Lycoris with a strong sense of purpose and a penchant for perfection. Unfortunately, a hostage situation tests her patience, and the resulting act of insubordination leads to her transfer out of DA. Not thrilled about losing the only place she belonged to, she reluctantly arrives at her new base of operations—LycoReco, a cafe in disguise. Takina's new partner, however, turns out to be quite different from what she imagined. Despite being the famed Lycoris prodigy, Chisato Nishikigi appears almost unconcerned with her duties. She drags Takina along on all kinds of odd jobs under the simple explanation of helping people in need. Takina is even more puzzled when Chisato takes down a group of armed assailants without killing any of them. Feeling like a fish out of water, Takina itches to get reinstated into DA—but Chisato is determined to prove to her that there is more to a life than just taking them.

Mithril, a covert military institution using state-of-the-art technology to combat terrorist operations, assigns a specialized team to a sensitive mission. Under the command of superior officer Melissa Mao, sergeants Sousuke Sagara and Kurz Weber must secretly protect Kaname Chidori—a teenage girl who unconsciously holds breakthrough scientific knowledge and is considered a Whispered—from intelligence agencies and other organizations pursuing her abilities. While Kurz and Melissa are to assist him remotely, Sousuke enrolls at Kaname's high school as one of her classmates to closely monitor her. However, his militaristic upbringing and poor social skills lead to a difficult adjustment to civilian life. Not only does he attract unnecessary attention, but his actions frequently make Kaname suspicious of him. Despite the earnest attempts to fulfill his duty, a terrorist ambush further complicates Sousuke's task. Recognizing the vicious mastermind behind the assault, Sousuke abandons his orders to ensure Kaname's safety.

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.