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My friends got me into TF2 and I couldn't stop thinking about THIS.
I think the fandom tends to depict Monogram a bit too harsh sometimes. I mean, sure, he doesn't pay Perry well enough and doesn't give him much free time, but that's not necessarily up to him. He's constantly praising and congratulating Perry even for smaller accomplishments like making a cool entrance into the lair or wearing a good disguise.
He worries for him and asks him to be careful during missions.
He organized a birthday party for him even if he got the dates mixed up.
He was literally bawling his eyes out when Doofenshmirtz made all those clones and framed Perry for evil, and he was crying in happiness when Perry proved his innocence.
Sure, he's far from perfect both as a boss and as a person, but he is trying, except maybe the way he treats Carl. That's pretty messed up. But I think he genuinely cares about Perry. He knew him since he was a little baby platypus and watched him grow into the best OWCA secret agent. Of course he's proud of him.
Also, Perry is far from submissive. He respects Monogram to a certain degree, but he won't hesitate to let him know exactly how he feels. Monogram knows what each sarcastic look and side eye Perry gives him mean and acknowledges his opinions and objections.
My point is, Monogram and Perry might be boss and subordinate, but in a very casual, chill sort of way.