I think the Doomsday machine is not something either Walter or Walternate constructed. I believe it is something Walternate found. He told Peter it was very old tech, which leads me to believe it was the invention of the First People who appear in the red-tinged opening credits for Over-There-Fringe. Several vague references have been made to their not being the original inhabitants of this world, so I think Walternate is attempting to awaken an ancient weapon.
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