Think about it-the flashback showed the Major, all beaten-up and bloodied, with what looked like a Tokarev (Russian WWII-era pistol) held to his head.
The Doctor is allegedly the one turning people into vampires, but we don't know how. Without the Major, the Dok would have no authority over Millenium. So maybe he cloned/built a robot of/cyborged back to life the Major so he could continue his plan. Remember, the whole Order 666 by Hitler made the Major the absolute boss.