I believe that Agent Maine started off in the SPARTAN Program, and was then transferred into Project Freelancer.

How else could he be so tough? If he isn't a SPARTAN-Freelancer hybrid of some kind, I don't know what he is.

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Project Freelancer is a Private project subsidized and funded by a mix of Government funds, research grants, and shell corporations. They function separately from the Government and as such don't take recruits from the UNSC or UEG Police forces. They recruit from Mercs, Veterans, misguided soldiers, and recruiting centers.

The SPARTAN project was TOP SECRET government/ONI initiative headed by Catherine Halsey for the explicit purpose of creating a genetically perfect Super Human counter terrorism team (essentially) and had no outside funding. It was all done through ONI and the UNSC Naval Warfare Research and Development group.

So no, Agent Maine couldn't be from the spartan project. Before you question the strength, remember the armor they wear is a REACTIVE armor that increases their natural abilities, and the UNSC did have genetic engineering on a smaller scale, Marines recieved minor gene tailoring to assist in prevention of Muscle deterioration from extended space flight, and ODSTs recieved minor enhancements to their endurance and musculature.