Are there any Star Trek episodes in which the bad guys looked human and the good guys looked very alien?

Question

My recollection is that in Star Trek, physical appearance is often a clue about the character — I heard about "Red Shirts" years before the Internet and the deep exploration of Star Trek lore that it allowed.

It seems to me that in every case I can remember, if there were two alien species in opposition, the species that looked human were the ones the Federation, or at least the crew of the Enterprise, aligned themselves with.

But was there an exception to this, where the bad guys looked human but the Enterprise's crew looked deeper than this?

Answer 1

The Voyager episode Nemesis fits:

Chakotay's shuttle has been shot down, leaving him stranded alone on a jungle planet. He is captured by troops of the humanoid Vori species, led by Brone (Michael Mahonen), but they appear to release him when they determine he is not of the "nemesis". Chakotay and a Vori look for his shuttle the next day and encounter two of the "nemesis". They are known as the Kradin, who are fierce, monstrous-looking, and technologically-advanced humanoids.

The Kradin explain that they are battling a relentless force called the Vori, whom they also refer to as "nemesis". Tuvok goes down to the planet and rescues Chakotay, who has actually been experiencing an elaborate training and brainwashing program to turn him into a Vori foot soldier. He has been thoroughly indoctrinated to believe the Kradin are monsters and is disgusted by the sight of them. Once Chakotay is back on Voyager, he is presented with evidence that the Kradin are not necessarily the hateful monsters he thought them to be, as Captain Janeway confesses to uncertainty concerning the right and wrong of the conflict, and that it was in fact the Kradin who helped locate the commander and return him to Voyager.

The kidnapping/brainwashing Vori look like this

The Kradin who returned Chakotay to his ship look like this

Answer 2

• TNG, "Home Soil": the good guys are a sentient mineral life form. The bad guys are the Federation themselves, who are destroying the mineral life in the process of terraforming their world...unknowingly, but with some degree of willfully ignoring the evidence that the mineral life exists. In the end, Picard negotiates an agreement with the natives to put their planet under quarantine.
• Voyager, "Scorpion": the good guys are a non-humanoid lifeform from another universe with drastically different properties, who are defending themselves from the mostly-humanoid Borg, a particularly attractive example of such being chosen as representative to the Voyager crew. Janeway allies with the Borg and develops a potent nanite-based weapon against the species they attacked. The two humanoid factions end up in conflict at the end, but the sole surviving Borg (the attractive female human one) ends up becoming a permanent member of the crew.

Answer 3

In addition to other fine, more specific answer - I'll give a more general, and controvertial answer: Probably about every other episode of Star Trek TNG and Star Trek DS9; and that's because Star Fleet are bad guys.

No, I don't mean in the Mirror Universe (which could also serve as somewhat of an answer to your question) - I mean the regular one.

You see, Star Trek as a show is mostly a self-narrative of the United Federation of Planets, or rather of specific crews of ships or bases within Star Fleet. It's true that the show is written by real people on Earth in the 20th century CE, but they are choosing protagonists for their stories and describing them, or self-describing them, as the good guys. Unfortunately, that kind of flies in the face of facts (facts-in-the-universe-of-the-show of course).

I won't go into an entire dissertation of why the UFP is an evil empire, but in a nutshell:

1. Human-supremacist civilization
2. Privileged populations (e.g. on Earth) live lives of luxury and leisure while on most planets people need to work to make a living
3. Huge parts of civilizational activity militarized fully or mostly: Foreign relations & diplomacy, scientific research, interstellar travel
4. Civilian political structure flimsy and of little consequence, exerting no control over the military which effectively holds sovereignty
5. Somewhat expansionistic

Point (5.) is actually the more difficult to demonstrate and argue for, but it's certainly the case if you look at Bajor. Even though supposedly that's not a planet which meets the criteria for entering the federation, it manages to strong-arm the Bajorans into letting it control a choke point for interstellar travel and commerce, by a military governor, with that governor also heavily interfering with Bajoran politics and religion. The Federation acts with the clear intent to take over Bajor, in the practical interstellar sense even if not formally through federation membership (which, recall, means loose subservience to Humanity and Earth).

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You may want to check out this article about how the Federation is an evil empire (which not exactly my view, but somewhat close).