The Beta programs are various illegal projects to exploit viral reprogramming of the human genome to create superhumans. The object of these programs was to develop super-soldier-spies.
Integration into the Bourne films
The Beta programs are retconned into the Bourne film continuity in The Bourne Legacy, as the reason why Jason Bourne is a superior subject as compared to the average teams and spies. He is retconned to be a Beta-I series project subject. All Operation Blackbriar and Operation Treadstone operatives are retconned to be Beta project subjects, Blackbriar operatives being Beta-II series.
The program originated in an accident at USAMRIID at Fort Dettrick, when Dr. Dan Hillcott examined the five dead scientists after a viral accident. He discovered a way to modify the human genome. This lead to his collaboration with Dr. Albert Hirsh to create the foundation of the Beta programs. The programs modified human cognition (blue pills) and human muscle power (green pills). Eventually these could be obviated by full viral modification of the human genome, and permanent enhancement, but it resulted in a severe flu-like condition, where the subject could die. Dr. Hirsch is part of the Black operations side of the government, while Dr. Hilcott works at Sterisyn-Morlanta (a Candent Group company). The pills are manufactured by Morlanta Pacific in Manila, Philippines. The entire Beta programs are overseen by the National Research Assay Group.
The first project in the program was Emerald Lake (Beta-0 series), the original of the enhanced spies. They used two viral factors to induce increased muscle and cognition abilities. However withdrawal of the viral factors led to loss of the skills imbued by the viral factors, necessitating the need to keep popping the pills. The loss of the cognition factor led to a decline in baseline cognition below that of the subject prior to induction into the program.
After Emerald Lake, several Beta-I series projects were initiated, for the Black programs, JSOC, and the CIA. The CIA program was Treadstone. These improved programs still had bugs to work out. The next step were the Beta-II series projects.
LARX was Treadstone without the inconsistencies, Outcome without the emotional attachment, and was the latest Beta-III project, which has only recently come online as of The Bourne Legacy film.