The story told to people is that the Athena Plan is a project with the goal of educating gifted children. However, the true goal of the plan is to gather orphans with exceptional abilities to be developed as governmental tools for whatever purposes the government deemed fit. The children were taken to an institution known only as The Settlement and their original identities supplanted by numbers. Afterwards, these children were never heard of again.
The project was based on a new drug accidentally developed by a Japanese pharmaceutical company that was engaged in brain function research in the mid-90s. The Rising Peace Academy focused on that research and launched the Athena Plan. Pharmaceutical companies, neuroscience research institutions and state-of-the-art medical organizations were involved in this project. The plan itself was terminated seven years ago.
The Athena Plan was implemented as people wanted to make Japan a truly independent country. Its real goal was to reproduce the Savant Syndrome artificially, creating humans with abilities beyond the norm and raising personnel more useful than any weapon. The Savant Syndrome is a condition where the brain function is extremely high, but only in a specific area.
A total of 26 children (all of whom were test subjects) were gathered in the Settlement, which is the place they were brought to. Vast amounts of research funds were poured into the Settlement and many talented researchers were brought there as well. However, the new drug (see History) was only effective on developing children under the age of five and was not permissible for use on a regular person's body and mind. The bodies and minds of many subjects were ruined, and most died.
In the end, the Athena Plan resulted in failure and was discontinued seven years ago after the U.S. government (who had become aware of the Plan) had intervened. By the end of the experiment, only a single child survived (Five) and an American agency took custody of her. However, two children escaped by starting a fire and disabling the security systems. The person in charge of the Plan was Dr. Mamiya (i.e. the person who "killed" himself, but Shibazaki didn't believe that).
The two children who escaped were Nine and Twelve (who, as stated before, started a fire and disabled the security systems in order to escape). They eventually returned to steal the atomic bomb, the thing that they least wanted to be known for, in order to commit patricide and kill everyone involved in the Athena Plan. The Plan's drugs also affected Nine and Twelve. In the last episode, Nine dies because of the effects of the aforementioned plan.