Although primarily an action-comedy cartoon, Atomic Puppet isn't afraid to pull off the occasional emotional moment, particularly when it comes to Captain Atomic's difficulty with accepting his transformation into AP.
- Joey and Pauline's friendship falling apart in the Bad Future presented in "Hero's Holiday".The shot they use really works for it.
AP: What? And pretend things are the same as always?! One day, Joey, when you get a little older, you'll learn that friendships don't last forever. Things change. (storms off to his old headquarters and lies down under a box of his old stuff) *sigh* What did I do to deserve this?...
- AP's bitterness over his transformation into a sock puppet during the Justice Alliance Christmas party.
- The Ghost of Holidays Past, Present, and Future showing AP his actions, like with Mookie and calling him out for how treated Mookie. Given that the ending reveal that the Ghost was actually a manifestation of his inner voice, it's clear that AP really came to regret how he treated Mookie.
- In "Worm Boy", AP is furious about Joey's new powers because it means they can no longer become Atomic Puppet and he makes a big stink over it. However, when Joey leaves to follow the mysterious insect swarms, AP shows his true colours, grabbing a photo of him and Joey and glumly saying "I can't believe he went without me." The guy's a lot more sensitive than he lets on.
- AP's fears that the Justice Alliance won't accept him back in their ranks in "Justice Alliance".AP: You don't understand, Joey. I was Captain Atomic! Those guys looked up to me!
- AP's pity party in "Private Proton" weirdly borders on being funny due to how overdramatic he is in the whole thing.
- Phil's reaction of horror as he helplessly watches Joey get the crap beaten out of him by Professor Tite-Gripp and Mookie in the climax of "The Big Shift".Phil: Son...
AP: I can't let them think Mookie threw me into the sun! They have to know the truth!
- In one quick shot in "The Big Shift" while at the pancake house, AP can be seen unhappily staring into a toilet bowl at his reflection. It briefly transforms into that of Captain Atomic as he silently reflects upon how with the first year anniversary of Atomic Puppet, the people of Mega City will stop wondering what happened to Captain Atomic and never learn the truth.
- AP having to accept the fact that telling the truth probably wouldn't be much better than letting everyone think Mookie killed him.
Joey: And what is the truth?
AP: *sighs* He turned me...into a puppet.
- In "Bucket List", AP admits to Joey that he wanted to travel through time to warn his past self about being transformed into a puppet by Mookie.AP: Look Joey, if you could tell your past self to avoid becoming something you didn't want to be, would you do it?
Joey: Yeah,...but I was hoping you started to like being Atomic Puppet...*sighs* We should never have done this list (takes out the challenge list, crumples it up, and tosses it aside)