When the US joined WWII, a famous and crucial race began. Which country (or side) would develop a nuclear bomb first. In the US, this project was called the Manhattan project. This is why Moore named Jon 'Dr. Manhattan'. He is subconsciously connecting him to nuclear power before the reader has any physical evidence. This act also indicated that the USA planned on using Manhattan for violent acts. This hinted to other countries that unless they themselves became savvy to nuclear technology and informed the world of their new power, the US would take over the world. The US government actually brought on the war with Russia themselves.
Link:
http://www.atomicmuseum.com/Tour/manhattanproject.cfm
and what are the implications of connecting him to that idea so immediately?
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