Zartan fluctuates between caring for Zarana's well-being to barely caring what happens to her. This could be written off to bad writing, different writers, etc. However his initial filecard said he suffered from schizophrenia and multiple personality disorder, while the fiction has even gone so far as to state he no longer remembers his original identity or personality. His mood, thoughts and feelings are highly inconsistent so his attitudes towards even his family would also be inconsistent.
When Scarlett and the Duke android fight in "Synthoid Conspiracy". Imagine if they were real people: She knows he's a fake by then, but it's still a young woman beaten up and almost killed by someone who looks, walks and talks exactly like the man she loves, down to the smallest detail. Of course, she's saved before he does any permanent damage to her, but even so, what does that (realistically) do to her psychologically? Will she ever feel safe with Duke again?
"Glamour Girls," when Cobra kidnap auditioning young model hopefuls to feed to a latter-day Countess Bathory expy. This is obviously pretty bad in itself, but if one ignores the fantastic life-draining aspect, the episode reads very much like Cobra are running a human trafficking ring.
Extensive Enterprises. GI Joe knows this massively corrupt MegaCorp is run by Cobra, but they apparently can't shut it down. Only two explanations for this are possible. Either Washington is so corrupt in this setting that the government protects a company that finances domestic terrorism. Or, even worse: Cobra is so powerful that they can lean on the government to stay out of their business.
That last bit must be true, anyway. Cobra semi-regularly launches full-blown military attacks on domestic targets in the CONUS, with air support and armor, and the government is by all accounts either unable or unwilling to stop them. So, imagine what a Crapsack World this universe must be: The United States is subject to air raids by an N.G.O. Superpower of fascist terrorists, like Yemen or Pakistan are to American bombings in real life. And then you remember their world also has giant robots from another planetandgiant monsters from the center of the earth running around...
The Cobra Academy, which turns out the elite of Cobra's troops. It's run by a dishonorably discharged ex-Marine who is an exemplary soldier and brilliant officer, but who was run out of the Corps because he is also a bully and Sadist who injured, abused and extorted his own classmates as a cadet. Now he's in charge...
Really, a lot of Cobra's cartoonish villainy becomes this if one stops to think about it. For example, having unarmed captives fight wild beasts for entertainment? Within the limits of the show (where, of course, nothing graphic happens) this makes for an exciting scene; taken seriously, it means that the Cobra leaders are depraved sadists on par with the nastier Roman emperors, who enjoy seeing people horribly mauled and eaten alive.
Lady Jaye is a bastard daughter of the McCullen clan, which Destro is the head of, which means she has the taint of the Old Ones' Villainous Lineage. Suddenly, all her improbable survivals and extreme physical feats in the series take on a new and more frightening significance...
In the animated movie, the reaction from various characters of seeing Cobra Commander after his exposure to a spore pod.
Also in the movie, what all the Joes captured by the "trees" may have gone through, could those trees have had some kind of anaesthetic effect, like when a close up of Scarlet later is shown with her eyes closed, or could they, especially Roadblock's detachment from earlier, have been awake the whole time?
In "The Traitor" Duke schemes to sabotage large amounts of Cobra's arsenal by letting them have the Joe team's secret armor formula, which he knows is unstable and thus unreliable. A lot of Cobra equipment is ruined, which is cool and all, but what if Cobra actually found a way to stabilize the armor formula?
In the third season of The Transformers, which takes place in 2006, the one off character "Old Snake" is revealed to be Cobra Commander himself. Everything he's done and he's a Karma Houdini.
Cobra launches a televised Cobrathon to finance the construction of their supercomputer. The broadcast can't be stopped and people actually donated their money. It went so well that they actually reach their 5 billions dollars goal, at least until G.I. Joe put a stop to it. Even among criminals, what kind of crazed maniacs give their money away to a terrorist organization like this?
