Project INDIGO

It has always been a difficult task keeping track of just how many augmented operatives are in the field, given the number of different projects. With Project ORION, which produced the original SPARTAN supersoldier test candidates who would serve with distinction throughout the Insurrection and in limited numbers during the Human-Covenant War, many retired from service or were discharged due to adverse psychological or physiological reactions to the augmentations and the operations they were deployed on. The SPARTAN-III Program has become notorious among Beta-5 personnel for it's personnel problems, with operatives turning up in classified Headhunter teams, or even reassigned to other chains of command, such as the case of Noble Team. Indications exist that other experimental augmentation programs were set up by ONI, but none ever achieved the success and fame of the SPARTAN-II Program.
Even here, there are factors that make pinpointing just how many SPARTAN-II personnel are still active difficult to discern. The program itself lists all deceased personnel as Missing In Action, rather than Killed In Action, for morale-improving purposes. At least some of the personnel regarded as MIA have turned up elsewhere - Kurt-051 was abducted for the SPARTAN-III Project, while Grey Team are still missing, presumably behind Covenant lines. Of the original 75 SPARTAN-II candidates abducted and trained, only approximately 35 were deemed successes after the augmentation process. Many of the other candidates were either killed, or physiologically deformed. At the same time, however, the existence of other SPARTAN personnel outside the regular chain of command means that ONI has hesitated to regard all of these as failures - Black Team was deemed among the candidates killed during augmentation, and were eventually discovered to have been operating in the field since that time, testing prototype equipment. Likewise, other personnel with impairments just as serious have continued to serve, using cybernetic enhancements or flash-cloned and re-augmented replacements. Even among those genuinely considered MIA, there must be some doubt - ONI has proven its ability to create elaborate cover stories for high-value personnel it wishes to reassign without links to the original unit. Further complicating matters are personnel with designation tags higher than the supposed 150 limit, such as Ralph-303 and Andrew-306, an indication that some ambiguity was intended by Doctor Halsey herself. 
Whatever existed of the original Project INDIGO, very little of it has since been uncovered by ONI Operative 1132267 - Mike Golf Papa (SHOGUN) in his investigation, codenamed Operation: VORAUSSICHT. There are indications that it resulted in more than one team of SPARTAN-II personnel assigned to duties outside of Doctor Catherine Halsey's sphere of influence, and Black Team's disappearance may be part of this. What is known for certain, however, is that it resulted in the formation of at least one team, Indigo (name unrelated to Project INDIGO) consisting of three SPARTAN-II's who would all be genuinely regarded by the SPARTAN-II Program project head as wounded, missing or deceased. Laura-125 was injured during the augmentation procedure, her expanding neck muscles contracting around her throat, nearly crushing her neck - doctors managed to save her life, but were unable to save her voice. Unwilling to assign a mute SPARTAN to combat duties, Halsey assigned her to a non-combat role assisting technicians in conducting field tests. Her recruitment was a straightforward matter - the operative, codenamed PRIVATEER, approached her, offering her a combat role. She accepted. Paper trails were falsified, but Halsey had already lost interest, moving on to advanced development of MJOLNIR improvements, retrofits and replacements.
The recruitment of her two team mates, however, was more complicated. Jeremy-068 was a successful augmentee, but suffered a myocardial infarction. Medical staff on hand were unable to revive him, and he was pronounced dead. To the surprise of ONI, not to mention the morgue staff, Jeremy revived after just under an hour without his heart pumping, suffering from no ill effects - an opportunity that ONI simply could not pass up. Officially, Jeremy is still classed as among those killed during the augmentation process. Informed of the fate of the failed augmentees, Jeremy became disillusioned with the Doctor Halsey, willingly joining Project INDIGO. Andrew-306, on the other hand, suffered no such drawbacks. He was initially approached by PRIVATEER after augmentation, confronted with the fates of the "failures". When he proved sympathetic but unmovable, PRIVATEER disclosed that Jeremy was still alive, and Laura had recieved a combat position - choosing to join his team mates in INDIGO, he reluctantly allowed himself to be transferred. Andrew's "death" was engineered by ONI, using a live fire exercise and careless personnel as a cover story - in fact, VORAUSSICHT uncovered that the "story" may have been a genuine attempt to kill Andrew by either Insurrectionist sympathisers, or a rival of Doctor Halsey. Regardless, as far as the other members of the SPARTAN-II Program are aware, Andrew was killed in 2525.
There are indications that Project INDIGO, and codename PRIVATEER, had their hands in other projects as well, such as the previously mentioned Black Team, as well as later SPARTAN-III initiatives such as Noble Team and the Headhunter teams. VORAUSSICHT was unable to find any concrete links, and only uncovered the existence of Indigo Team by a chance meeting between SHOGUN and Andrew in combat. Although both Baselard and Kukri teams were considered as a successor to the initial Project INDIGO, questioning of CAIN by SHOGUN indicates that the link is tenuous at best. Certainly INDIGO continued to run Indigo Team's operations until it disappeared in 2535, when Beta-5 took over Indigo's handling, and formed a lasting relationship between Indigo Team and the VAJRA-II sub-cell developing prototypes for the Mark IV and later Mark V, with Indigo testing many early equipment designs and prototypes in combat. Afterwards, there is no trace of Project INDIGO.
Investigations by SHOGUN were instigated by OLYNDICUS after becoming suspicious of his predeccessor as ONI Deputy Director of Operations, OZYMANDIAS. It has been proven that OZYMANDIAS was certainly involved in a number of ethically questionable activities, but there has been no proof that he was involved in Project INDIGO, or any of the other unauthorised augmented supersoldier programs.