With the intervention of the’super-soldiers’, the original plans for colonization seemed to be back on track with or without help from a shadow government of humanity.
The Return of CSM – Despite the end of the Syndicate, CSM attempted to gather a new group of individuals to collaborate with the aliens and restart the project. The crash of another UFO in Oregon seemed to be the perfect way to do so. However, CSM–already weakened from cancer and experiments with hybridization–was blocked from realizing this goal by the betrayal of Alex Krycek and Maurita Covarrubius. His apparent demise (or as it turns out his escape to hiding) seems to have ended the original program of controlled alien invasion through mass infection.
End Game By this point well established in the upper echelons of the government, the super soldiers no longer needed co-conspirators as equals to maintain the invasion plans. Instead, they were able to keep the relevant government officials in check by fear of their unstoppable nature and the promise of special protection from the coming invasion in a secret bunker. They continued to build on plans code named “End Game” for preparation of the invasion at the scheduled date: 12/22/2012. As had already been forecast, this invasion was to coincide with an international pandemic which would allow the government to use special powers under the federal emergency management act to take over military control of the country and the world. Once done, the supersoldiers and the aliens could come forward and take control.
Reprieve? – The “End Game” armageddon never came to be. Why not is pure speculation because the next time we see Scully and Mulder in 2008 they are casually lying low in isolation with Scully going back to work as a doctor and Mulder holed away clipping intriguing tales from news of the weird. The FBI seems to have lost its menace—there is no fear of super-soldiers in their interactions. Though the ultimate victory of the aliens had seemed overwhelmingly unstoppable six years before, it would seem that individuals like Mulder and Scully found a way to use the knowledge they had gained of the aliens’ locations, their vulnerability to magnetite, and the influence of greater powers to overcome what seemed inevitable. Had the aliens left all together or simply faded into the background for another day?