The Vaccine is a creation of critical importance in the resolution of the Elfen Lied manga series. The Diclonius virus was derived from a woman, Kaede/Lucy/Nyu's mother, and then spread by her daughter, the 'Queen' Diclonius. She in turn created Silpelit carriers in the form of horned girls who further spread the virus, which, if spread far enough, could place the Diclonius in a position to replace non-horned Humans. Two facilities were founded to try and handle this threat, one being the Diclonius Research Institute under the control of the Kakuzawa family, who secretly believed they themselves were of Diclonius blood and wished the one species to replace the other. The other was more directly under the control of the Japanese government under an operation called Saseba. Both organizations were suspicious of the other, and work on a vaccine for the Diclonius virus began on each side in different ways and for different reasons. Saseba also prepared weaponry based on utilizing and combatting Diclonius vectors, also possibly to seize materials and research from the Kakuzawas. How the Kakuzawas came into the position to do all this politically or financially is never made clear. It can be speculated that their fundamental belief in their racial superiority drove them to constantly better themselves.
The Anti-Diclonius Birth Vaccine seen in the story had its origins as something Professor Kakuzawa came up with as a potential negotiating tool for maintaining his family's control over their vision of a world full of Diclonii. It was possibly also a hedge against the unpredictability of his father. After his death at the hands of Lucy , his assistant Arakawa was compelled to use his research to complete it, and found batches of files and samples in a hiding place her dead boss often used. Seeing it as her ticket to legendary recognition in the scientific community, she put up with the more loathsome aspects of her existence and closed in on making the vaccine viable, later completing it but keeping her progress a secret, knowing how ruthless Chief Kakuzawa was to those he no longer had a use for. She puts aside her qualms about working for a man who had a genocidal agenda against the Human race, feeling she would have her fame one way or the other.
Suspicious of the Kakuzawas and fearful of their own involvement with them being exposed, the Japanese government sent two separate spies to find files on the Diclonius virus at the Kakuzawas' facility, and most especially, files on a potential vaccine, which they rightly assumed the paranoid Kakuzawas would develop as a precaution. When the First Escort Fleet was sent against the island stronghold, it had orders not to destroy the facility till it could be combed for information.
The agent sent in to pose as Kakuzawa's operative encountered Arakawa during the final Diclonius uprising. It was during this time that Arakawa realized Diclonius could sense the vaccine, as she saw how Mariko clone Diana seemed to want it destroyed, even in her controlled state. The case containing the research and samples of the successful vaccine seemed lost for a time, and Arakawa left the island at the Agent's behest. Once onboard one of the First Escort Fleet's Vector Attack Crafts, Arakawa saw a readout showing hundreds of Diclonii converging on the spot where the vaccine had fallen, indicating to her that it had not been destroyed, as the Diclonii sensed its threat to them. Again with the aid of the agent, Arakawa and the vaccine made it safely to the mainland. All she had seen and done began to create profound regrets and remorse in her.
In the series' final chapter, Kouta notes that, despite the existence of the vaccine, many Humans were killed by existing Diclonius and those created by Kakuzawa's attempts to spread the virus. Further, a temporary world-wide birth ban was implemented until all infected could be vaccinated or sterilized. Arakawa gains the worldwide fame and adulation she once desired, but her experiences took away her enjoyment of it. The very end of the story shows that Kouta, who was likely among the many deliberately infected by Kakuzawa, now has a daughter who does not have horns, so it can be reasonably speculated that the vaccine was successful and the Diclonius threat defeated or reduced enough to lift the birth ban.