Yeah, switching minds with Norman McArthur (and thus condemning McArthur to death) is one thing, but brainwashing an innocent boy he'd "adopted" (and was apparently grooming as a genuine heir, as opposed to "Doom, Jr.") is something else.

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Doom's plan was to gather the molecules of his body from around the universe and transfer his mind back into his reconstructed body.  So even then, his plan wouldn't have condemned McArthur to death.  Of course, the Beyonder stuck his nose in before Doom could execute his plan ...