The government originally had a two-faced agenda in dealing with the aliens. They presented an attempt at a diplomatic deal with the aliens in the day of the young CSM and Bill Mulder. They also had a secret agenda directed more towards defense, should the surface deal fall through. this it did, evidently, with the advent of the black goo.

Humans did, in their early dealings, procure various alien technology: gene therapy, alien tissue, propulsion systems, etc. When the aliens began to show hostility (or at least breaches in the deal), however, the Majestic Consortium decided to abandon any attempt at friendly communication. By this time, they had gained the technology to start hybridizing humans with aliens, though they didn't necessarily want to do that for the reasons they are doing it now. The aliens obviously had technology far superior to ours, so the Consortium was at aloss at how to defend earth from absolute colonization (presumably because earthlings haven't taken care of their home and aliens think they can so a better job). This led to a more directed attempt at hybridizing. These new hybrids (the ones with no eyes and no mouths, as shown setting people on fire in recent episodes) are the Earth Resistance Force. They are not renegade aliens, they are freedom fighters for earth, using their super human capabilities along with transportation obtained from aliens since the 40's to try to stop the colonization.

The Consortium, therefore, is not as evil as people once thought. They may have started out evil and underhanded, but when earth became endangered, they switched to good (or as good as they can get, at least). The basic point is they have the earth's and humanity's best interests in mind. I don't know what Deep Throat and X have to do with it (although if X, Deep Throat and Bill Mulder were in fact once part of MJ-12, then that would make 12 guys...), but they evident'y have a few extra scruples as far as the truth goes.

• Scott Glancy's Conspiracy 101
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