Phlox is feeding his pets, when Hoshi enters with a letter from his exchange doctor Jeremy Lucas, who is serving on Phlox's planet. Phlox begins writing a letter to him about the ways humans and Denobulans are different, also suggesting that Cutler has a crush on him.
On the bridge, the crew has found a pre-warp vessel, that doesn't respond to hails and has two weak bio-signs on it. They dock the vessel and take the aliens to sickbay, where one alien begs for medical attention as their species (called Valakians) is going extinct. When they reveal that despite being pre-warp, they've met warp-capable species and know all about warp drive, T'Pol agrees to help them. Phlox describes the situation in his letter, noting that it started as humanitarianism and was the greatest dilemma he'd ever faced.
In the mess hall, Hoshi, who is learning Denobulan, discusses the situation of Cutler's crush in a combination of English and Denobulan with Phlox. The Enterprise then arrives at the Valakian home world, where Archer, T'Pol, Phlox, and Hoshi tour the medical department. Hoshi discovers that there is another species on the planet called the Menk, who aren't as advanced as the Valakians and are immune to the disease.
Phlox continues his letter, describing the challenges of finding a treatment for the disease and conversations he'd had with T'Pol about interspecies relationships. He finds out that the disease is not a pathogen but rather genetic, and that he does not know how to cure it.
While Phlox continues searching for medical information, he finds learning about the Menk and Valakians' society exciting. When the Valakians reveal that they do all the farming, believing that they could do it better than the Menk, Hoshi disapproves of this, believing the Menk are being treated like "pets", but Phlox just believes it's good that the two species are, for the most part, getting along. While visiting a Menk city, Phlox, Hoshi, and Cutler find out that the Menk are capable of learning English and organising tissue samples.
When everyone packs up, Phlox asks Culter if she is indeed interested in him, and she affirms. He reveals that he has three wives, and each wife has three husbands. Cutler says that she doesn't want to marry Phlox, but likes him as a friend and isn't opposed to dating him in the future.
Archer visits the first alien he rescued in the hospital. The alien asks Archer for warp technology so that they can search for other species who can find a cure if Phlox fails. Archer returns to the Enterprise and finds out that they've received 29 hails from other clinics, all requesting help, and has been approached by two vessels who thought they already had a cure. In the ready room, Archer talks to T'Pol about how he's not so sure about giving them warp technology, since they have no experience.
Archer and Phlox talk over the situation at dinner in the mess hall. Phlox thinks that it would be best not to cure the Valakians since he believes that the genetic disease is an "evolutionary dead end" they've hit, and that the Menk need to advance and will only do so without the Valakians. Archer disagrees, but Phlox, despite being revealed to have found a cure, is adamant that he not give it to them.
The next day, at the hospital, Archer now agrees with Phlox not to cure the Valakians as that would be "playing god". However, they do give the Valakians medicine for the symptoms. Phlox finishes the letter and goes to have dinner with Cutler.
- Aborted Arc: Phlox and Crewman Cutler flirt with each other this episode, but nothing comes of it in later episodes. Her actress, Kellie Waymire, would later die during the filming of Season 3, but Cutler had already stopped appearing after Season 1.
- Alien Non-Interference Clause: At first subverted; since the ship encountered was explicitly looking for help and the M'klexa and Ferengi have already dropped by, even T'Pol thinks it no longer applies, so an away team visits the planet to learn more about the medical crisis. After discovering its cause and a pitch by Phlox that they shouldn't interfere, Archer eventually decides against helping the Valakians since "we didn't come out here to play God." Notably, they couldn't have done this in any other series of the show, since the Prime Directive has been established to have an exemption for people who actually ask for help.
- Appeal to Nature: Doctor Phlox argues against curing a disease affecting the Valakians on grounds that the existence of the Valakian species is holding back the evolution of the Menk species on the same planet. He argues to Captain Archer that they should "let nature take its course". For icing on the cake, Archer's closing monologue in effect claims this incident as the origin of the Prime Directive.
- Artistic License Biology:
- Evolution leads species to inadvertent extinction all the time, usually from something like overspecialization, such as a single species parasite being out of luck if that species itself goes extinct. But the idea of a straight up genetic disease, somehow treatable with antibodies yet interfering with protein production to the point of death, spreading enough to doom an entire species, is simply nonsense.
- Phlox believes, based on scant and untested evidence from less than 2 days of information gathering and genetic profiling, that the Menk will someday be the dominant sentient species on the planet if the Valakians go extinct. But assuming future evolution from current trends, and making a medical conclusion based on that, is extremely arrogant and shortsighted. In addition, evolution has competition as a large component; far from 'holding them back', their relationship with the Valakians could in fact be what is driving the Menk to become more intellectually sophisticated, and Phlox is in fact dooming both species.
- Conflation of theory and Scientific Theory on the topic of evolution, but reversed from the usual misconception that evolution is 'only' a theory; Archer (accurately) says that the conclusions of Phlox concerning the relationship of the Valakians and Menk are only a theory, which Phlox in his response dismisses by deferring to the Theory of Evolution. This is a non sequitur, since Archer was clearly using the term generically to refer to what in scientific parlance would be a hypothesis, something which needs testing and is certainly not a final conclusion.
- "Blind Idiot" Translation: Hoshi accidentally asks Phlox if he and Cutler are "mating" instead of dating in Denobulan.
- Blue-and-Orange Morality: Lampshaded by Phlox to Cutler, but the main dilemma is a fairly straightforward medical ethics clash between human and Denobulan perspectives.
- Bookends: The episode opens with Phlox coming into his office saying good morning to all his animals and ends with him going out, turning the light off, and saying good night.
- Call-Forward: The Ferengi are briefly mentioned as having visited the planet, though no one recognizes their name.
- Culture Clash: Phlox is a bit wary of this happening with Cutler.
- Exotic Extended Marriage: Phlox reveals that this is standard on Denobula. He has three wives, each of whom have two husbands in addition to him.
- Foreshadowing: Any longtime Trek fan will know exactly what Archer is hypothesizing for the future.Archer: Someday my people are going to come up with some sort of a doctrine: something that tells us what we can and can't do out here should and shouldn't do. But until somebody tells me that they've drafted that directive, I'm going to have to remind myself every day that we didn't come out here to play God.
- Framing Device: The episode is loosely framed by Phlox's letter to a colleague.
- Friends with Benefits: Cutler has no objection to an interspecies fling with a married man.
- I Can't Believe I'm Saying This: Regarding the dilemma of whether and how to teach a species to build warp engines, and the irony of facing it despite disliking perceived Vulcan foot dragging on that very same topic.Captain Archer: I never thought I'd say this, but I'm beginning to understand how the Vulcans must have felt.
- Interspecies Romance: Cutler, a human, has a crush on Phlox, a Denobulan.
- Mating Season Mayhem: Discussed. Jeremy Lucas is on Denobulus during mating season and apparently things are very complicated and chaotic.
- My Hovercraft Is Full of Eels: When Hoshi tries to speak Denobulan she first calls an eggplant a "nostril" when meaning to call it a fruit, then she accidentally says that Phlox and Cutler would make a cute "washboard" instead of a cute couple.
- Nature Lover: Phlox says that Menk as a whole seem to enjoy growing plants.
- Offscreen Inertia: Since this episode is the first and last time we see these species, it is commonly assumed that the decision by Archer to not offer a cure at the end means that the Valakians were doomed to extinction. However, this is all being filed in his reports to Starfleet, which the Vulcans read. Archer himself says that they may still figure it out for themselves with the treatment information he does give them buying them at least a decade to do so, and Phlox earlier said that the timeframe for complete collapse was a couple centuries. Archer's decision at that moment is therefore by no means the final word.
- Sand In My Eyes: When Trip cries during a sad movie, he doesn't admit it, instead pretending that something is caught in his eye.