The more I think about it, the less likely it seems like Dr. Manhattan is holding Veidt. The whole prison is a giant mind-#@#$, specifically designed to eat away at Veidt. Dr. Manhattan, despite his powers, had lost his ability to understand human psychology.
We only see the first letter of who Veidt's message was directed at "D". So it could easily be him trying to contact Manhattan. I like that Veidt isn't just on the moon with the ability to merely catapult himself to Earth.
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