Project Hercules was the code name for a top secret effort by the United States government in the 1960s to develop enhanced fusion (also called "super-atomic") technology for military use. The project was initiated by 1961, and based at San Lobos Atomic Research Facility outside Albuquerque, New Mexico. By late 1968, an enhanced fusion bomb had been built, and was prepared for test detonation.
Project Hercules came to the attention of the Beta 5 computer earlier in the year, and months later, Aegis agents Gary Seven and Roberta Lincoln discovered a Soviet spy ring in Albuquerque working to compromise the project. Seven and Lincoln then infiltrated the project, where they discovered the project head, Dr. Diana Winters, was in fact a deep-cover Soviet spy. In the wake of this discovery, Project Hercules was shut down pending an investigation, and never resumed. (TOS - Star Trek: Assignment: Earth comic: "Brighter Than a Thousand Suns")
Unknown to Seven at the time, the group Counter Strike had supplied advanced technology to the Soviets in order to prevent Aegis interference in the Hercules test. (TOS - Star Trek: Assignment: Earth comic: "We Have Met the Enemy...")