Commander Atomic is the villain of Atomic Puppet. He is the opposite version of Atomic Puppet.
He has the similar appearance of Captain Atomic, except he had dark purple incarnation on other parts of his suit as well as a demonic wings and horns on other parts of the suit. Another difference is that Puppet Boy is placed on his left hand than on the right, that which AP now occupies it.
He somewhat has the opposite of what AP's personality has, he will to do anything to mess around with Joey and AP's world, he and Puppet Boy both fear General Sub-Atomic, until it was the point of Mookie (who's General Sub Atomic look alike), had to play the part in order for Joey and AP to buy time while heading to Dr. Momus. He and Puppet booy were forced to do all the work that Mookie (As Mookay) commanded.
- He and Puppet Boy, being as polar opposites of Joey and AP, may be referenced as similar to them "Bizarro", in the Superman series where it is the same as the character, who also is the polar opposite of Superman itself.
- Despite of his appearance being similar to Captain Atomic (AP's former superhuman form), in his dimension, he was never turned into a puppet like Mookie did to AP, however this might of affected Puppet Boy, who might been originally a human, that might of turned into a puppet by someone unknown.