The Commander survived since the skydark by means of organ transplant, cybernetic enhancement and cryonics. He had plans to breed various forms of mutants to help him take control of the Deathlands, and return it to it's former predark glory. The man also considered himself the President of the United States. Ryan was sickened at what the man plans to do, and by what the man showed him. He killed the Commander, and several of the men under his command while inside the Rushmore facility. (Stoneface)

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