The Chrysalis Project was a scientific project for the genetic improvement of the human race, active from the late 1960s to May 18, 1974.

The project gathered many of the finest geneticists, microbiologists, teachers and other scientists of the time, who believed that humanity was too weak and too unevolved to run itself. These scientists hoped that by genetically engineering a new class of humans and sending them out into the world, they were help to create a free and open Utopian society.

However, the project's director, Sikh Indian geneticist Dr. Sarina Kaur, and her associates Dr. Donald Archibald Williams and Dr. Viktor Lozinak, planned instead to destroy the human race, using several thousand specially-prepared biowarheads from the Soviet germ warfare program, Biopreparat, loaded with a genetically-engineered strain of necrotizing fasciitis, a flesh-eating form of Streptoccocus. By doing so, they would clear the way for the Chrysalis children to take over. (ST - The Eugenics Wars novel: The Rise and Fall of Khan Noonien Singh, Volume 1)

Financier Ralph Offenhouse and other leaders in the business community provided much of the financial support for this project. This would later become a source of great shame to Offenhouse, after learning his son had become a casualty of the Eugenics Wars after he had died and been placed in cryogenic suspension. (TNG novel: Debtors' Planet)

The project was derailed when Gary Seven and Roberta Lincoln infiltrated Chrysalis, beamed out all the Augmented children to an orphanage, and destroyed the facility. In order to cover up the existence of Chrysalis, Prime Minister Indira Gandhi of India announced that the explosion was the nation's first experimental nuclear detonation. (ST - The Eugenics Wars novel: The Rise and Fall of Khan Noonien Singh, Volume 1)

In 2382, the Chrysalis Project was an example of genetic engineering brought up during a meeting between President Nanietta Bacco and Starfleet Captain Jean-Luc Picard when discussing the use of such techniques to aid the Andorian peoples procreation crisis. (TNG novel: Paths of Disharmony)