Alternate Character Interpretation: Majestic 12 gets one in their Splatbook for the Atomic Robo RPG, pointing out that their goal is ultimately to protect people from dangerous superscience, and that they sacrifice a lot to do so:
Maybe you're used to seeing them as antagonists, but that's in the pages of Atomic Robo! Of course they look like bad guys there. We can't expect a book about Tesla's super robot to have the most nuanced view of a secret branch of the military dedicated to hunting down Tesla's most advanced technology. Majestic's agents are portrayed as a bit faceless, a bit fascist, and a bit trigger-happy. They strike with overwhelming speed, firepower, and numbers. And almost certainly without warning. Because that's what you've got to throw at a super robot if you're going to have any hope of stopping him! [...] On the other hand, if the idea of playing Majestic from the perspective of Total Science Bastards With Unlimited Gun Budgets sounds like a good time, then guess what, that works too!
Ass Pull: Projekt Longinus, a previous unmentioned, still functioning 70-year old Nazi Kill Sat that just happens to be what Team Tesla needs to kill a ten kilometer wide Biomega island. While normally there's a fair amount of set up prior to revealing the next Crazy Awesome piece of hidden history in the Atomic Robo universe, there's little hint of this beyond an offhand mention of "the Nazi space program" at the start of The Savage Sword of Doctor Dinosaur arc.
Crazy Awesome: Dr. Dinosaur. He's an insane, Mad Scientist dinosaur - resembling a species from Jurassic Park more closely than anything that actually existed - who claims to have traveled through time and space to destroy humanity and make dinosaurs rule the Earth once more. He's also appears to be invincible having survived shootouts and fistfights with Robo, getting smacked full-tilt by an armored truck, and being close to a bunch of grenades exploding and taking out Robo. He spends his time doing things like shooting up 4th grade science fairs to steal a little girl's experiment, buying guns by using a children's picture book as ID, and trying to kill Atomic Robo for little to no reason.
Ensemble Dark Horse: Jenkins, even though he is technically the main character's sidekick, is an unstoppable One-Man Army with hilariously overblown results and comically high-culture interests. Dr. Dinosaur is a hilarious one-off villain created for a free comic book day story who quickly became one of the hero's main antagonists.
Memetic Badass: Jenkins. Even the writer thinks he's cooler than the main protagonist. The Tabletop Game adaptation making him more expensive to play than the bulletproof, superstrong industrialist-adventurer he works for doesn't help.
Tearjerker: Robo and Tesla's falling out in "The Deadly Art Of Science".
The Reveal that Edison became evil because he wanted to be with his wife forever.
Robo ultimately Did Not Get the Girl as Helen ends up with Chen. He knows it's probably for the best as he is functionally immortal but it still doesn't lessen the blow.
There's an undercurrent of melancholy all throughout Knights of the Golden Circle. It starts with Robo having spent fourteen years alone in a shack in the desert in a time that isn't his, and then he reveals to Doc Holliday and Marshal Reeves that he's dying - he barely knows them, but he's got nobody else to tell. He goes down fighting, but it's hard to see his battered head put in a box to unconsciously take The Slow Path back home.
Robo revealing to ALAN 2.0 that he and Tesla fought before he went on his mission in The Will To Power - and that it was the last time he saw his creator alive.
Robo: I used to resent Mr. Tesla for keeping me cooped up.
ALAN 2.0: Was it also for your protection?
Robo: Yeah. We just had different opinions about how much protecting an invincible super robot needed. It was hard for him, and I never made it any easier. Hell, we argued about it the last time we spoke. The army said they'd make my citizenship "happen" if I just did one little secret mission for them. It was an offer I couldn't refuse. But Mr. Tesla was a pacifist. I'd never seen him so angry. And then I never saw him again.