Travis and Malcolm are playing chess in the mess hall, but they're both possessed by aliens. They're discussing the humans they're observing and wonder what will happen when they go to the planet, with "Malcolm" noting that at least one person always dies when they go there.
Trip and Hoshi are returning from a garbage dump on the planet, in a shuttlepod. Trip hails Archer, telling him that they found nothing except an old power cell, some empty ration packs, and a latrine. Then, he has a coughing fit and passes out. Hoshi tells the other senior officers about what happened to Trip and takes over piloting the shuttle.
Trip and Hoshi get put in decon, while the shuttlepod is checked, to make sure its environmental systems aren't what made Trip sick. Phlox, noting that other people have been to the same planet and been fine, gives Trip and Hoshi blood tests, when Hoshi starts coughing as well. Archer and Phlox leave, and Phlox notes that he's determined that Trip and Hoshi's condition is an infection, but can't determine the cause of it.
In another corridor, the possessed Malcolm and Travis talk about how the Klingons reacted to the same disease, with "Travis" noting that the Klingon commander didn't allow the sick people to beam back onto their ship, whereas Archer did. "Malcolm" says that that's not very noteworthy, since Trip and Hoshi are still being isolated from the healthy crew. "Travis" brings up the Cardassians, who, as it turns out, killed the infected crew, as did, eventually, the Klingons. "Travis" is hopeful that Trip and Hoshi may get better, but "Malcolm" is convinced they won't. "Travis" decides to talk to the sick people, while "Malcolm" speaks to Phlox.
Meanwhile, Trip and Hoshi have stopped coughing, and have developed body cramps, which they've been given medication for. They've also been given anti-nausea medication, as Hoshi had thrown up before. "Travis" comes and asks through a hatch what the meds are, but Trip doesn't know, since they're not diagnosed yet. "Travis" asks a series of questions about the two's history with illness, annoying Trip, who closes the hatch. In sickbay, "Malcolm" tells Phlox, who's analysing the blood samples, that he has a headache and looks at the scans of the blood. Phlox scans "Malcolm", determines that any headache he has is not serious, and gives him an analgesic. When "Malcolm" asks whether Phlox will make an antidote for Trip and Hoshi's virus, Phlox, believing that he's just afraid of contagion, shoos him out.
In decon, Trip's condition is stagnating, but Hoshi is slightly delirious. Trip is talking about a movie called The Andromeda Strain, about a virus, then he admits he used to get in trouble a lot at school. Hoshi admits that she was temporarily dismissed from Starfleet for breaking someone's arm during a game of poker. Phlox, meanwhile, finds out that the illness is a silicon-based virus which must have come from a meteorite (since only carbon-based life exists on M-class planets usually) and that his species haven't discovered it. He notes that Trip and Hoshi may die if he can't find a cure within five hours.
"Travis" is optimistic, since Trip and Hoshi have been diagnosed and haven't been killed or abandoned, but "Malcolm" is more pessimistic, believing that Trip and Malcolm will infect, and therefore kill, everyone else. In decon, Archer gives Trip some updates (Hoshi can't hear them because she's asleep) and tells him to get some sleep and stay positive, but Trip thinks he's a goner, since the human body doesn't reject silicon.
In the corridor, the possessed Malcolm and Travis start arguing over whether Archer is being rational— "Malcolm" thinks that by keeping Trip and Hoshi on the ship, he's putting the crew in danger of infection and doesn't know how serious the situation is, but "Travis" thinks that he's just being a devoted captain. They decide that in order to figure out how rational or irrational Archer is being, they need to possess someone new, so they choose Phlox and T'Pol, since Archer is making his decisions based on their findings.
In decon, Trip and Hoshi talk about how they're both jealous of each other's talents. Phlox and T'Pol visit, both now possessed, claiming to be checking up on them. Trip tells them to go back to sickbay and keep working, which they do. Hoshi wonders if their visit means that they're closer to finding a cure, but Trip still isn't as hopeful.
In the corridor, "Phlox" notes that Trip and Hoshi are being brave, but "T'Pol" points out that they're trying to figure out how smart the humans are, not how brave. "Phlox" says that "T'Pol" sounds as if she wants the humans to fail, but she replies that she just wants to see if they're smart enough to make first contact with. "Phlox", however, wants to judge the humans based on other factors than intelligence.
On the bridge, Archer and Malcolm find a crater on the planet and wonder if that's where the virus came from, and they contact the Klingons who went to that area, noting that if it is where the virus came from, the Klingons would likely be infected too.
When the test results are ready, the non-physical aliens decide to transfer to new hosts to allow Phlox and T'Pol to continue their work, so they jump back into Malcolm and Travis. Phlox and T'Pol look at the blood samples and note that the previous medication didn't work. T'Pol notes that the virus seems to be sensitive to ionizing radiation, but the necessary amount of it to kill the virus would also kill the patients. Meanwhile, Hoshi has woken up from another nap, during which she had a nightmare where she had insufficient time to tell her students goodbye.
On the bridge, Archer discovers that he has found debris from the Klingon ship, indicating that all the Klingons are likely dead, and therefore they probably didn't develop a cure. Meanwhile, Hoshi hacks the entrance to decon and escapes, all the while babbling in different languages. As she runs down the corridor, an alarm sounds, and "Malcolm" reports the quarantine breach. Hoshi reaches the airlock and tries to open that as well, with Trip pleading her not to do it. He fights with her and wins, then takes her back to decon. In decon, Trip tells Phlox that they're both back in quarantine, and Phlox tells Trip to inject Hoshi and then himself with something called "sonambutril". He complies and they both pass out.
The aliens possess Trip and Hoshi and talk about how it feels to be in pain. When Phlox sees them, they switch bodies and inhabit Archer and T'Pol again. They enter sickbay, where Phlox talks to them and then realises they're possessed. He asks the aliens if they're responsible for the virus, and "T'Pol" replies in the negative. She asks how he found out that she and Archer were possessed, and Phlox responds that he figured out Trip and Hoshi were possessed when they sat up despite being sedated, and then concluded that the aliens jumped to Archer and T'Pol. Phlox asks if they could help, but they say no, because they have a non-interference policy. Phlox points out that they're interfering with him, but they reply that they're studying humans, not Denobulans. They reveal that they possessed Phlox before, but erased his memory, so he asks if they could simply cure Trip and Hoshi and erase their memories, but they still refuse.
"Archer" wonders if Phlox has found a cure, but "T'Pol" points out that other crews had come up with the same cure, but too late. She then convinces him to switch back to Malcolm and Travis. Phlox and T'Pol then tell Archer that they've come up with a plan: use the bioscanner to make a precise amount of radiation to cure Trip and Hoshi's illness without killing them.
Hoshi's condition worsens, and she's taken to sickbay. Phlox and Archer attempt to revive her, even taking off their gloves to get a better grip and thereby risking infection, which the aliens note as unusual. The attempts don't work and Hoshi dies. "Travis", meanwhile, wonders why so many humans will have to die before "Malcolm" acknowledges that humans are "different". "Malcolm" retorts that the study isn't over since there is now greater chance of the virus spreading, and reminds "Travis" that they aren't responsible for the virus.
Archer and Phlox start irradiating Trip, then Archer puts Phlox on the bridge lest he get infected and puts T'Pol in command. The radiation doesn't work and Trip also dies. One of the aliens then possesses Trip and reveals to Archer that his species is called Organians. Hoshi is also possessed, and Archer and the two aliens discuss whether they should break their non-interference policy. Archer suggests that the aliens just talk to their subjects to give information, but "Hoshi" thinks they've advanced beyond talking. Archer disagrees, saying that seeing as the Organians have lost their sense of empathy, they're not more advanced than humans. Archer begins to get sick, and the aliens plan on leaving, but "Trip" refuses and insists on resurrecting Trip and Hoshi and treating Archer. Archer agrees, suggesting that this could teach them about empathy, which is a big part of humanity.
So, the aliens cure everybody. Archer tells T'Pol that Trip and Hoshi have gotten better, to the surprise of everyone else, whose memories of the Organians has been erased. He tells T'Pol and Phlox to come to sickbay, which they do, and Phlox scans the three, confirming that they're totally better. Archer decides to have the virus studied at Starfleet Medical and put a warning beacon up. The Organians, meanwhile, prepare to make first contact with humans in 5,000 years.
Tropes in this episode include:
- Alien Non-Interference Clause: The Organians have one, which forbids them from helping anyone infected with the virus.
- All Asians Know Martial Arts: Hoshi, the only main Asian character, is revealed to know aikido.
- Artistic License Statistics: The Organians claim 10123 permutations of a chess game is a limited number and thus chess is very predictable. In truth, even if every atom in the observable universe (roughly somewhere between 1078 and 1082 in number) had the processing power of the average Organian - even allowing for several sextillion calculations a second - and they had been calculating these games every second since the Big Bang, you'd still get nowhere near 10123 as a total. In short, 10 with 123 zeros after it is a BIG number.
- Bottle Episode: Second one in a row; this one uses only familiar sets (on Enterprise and the shuttlepod) and a few Ghost Extras. The Organians don't even need any special effects, only depicted as talking through whoever they possess.
- Call-Back: Archer mentions what happened in "Dear Doctor" while debating the Organians.
- Before leaving Enterprise, the Organians decide to draw up plans for an official first contact with humans.
- They also complain about the limitations of the chessboard. We see 3-D chess being played in TOS episodes.
- Apparently, the Cardassians had also visited this planet.
- A Day in the Limelight: Not for Malcolm or Travis, given that they're possessed by aliens every time we see them, but for once their actors get something to do.
- Dramatic Irony:
- Archer argues that the Organians should use their power to help instead of just observe. Kirk has the opposite attitude when he encounters the Organians.
- The two Organians muse that it will take 5,000 years to prepare for official first contact with humans. Viewers, however, know Organians will be revealing themselves to Kirk just over a century after this episode.
- Duct Tape for Everything: Joked about by Hoshi, when she claims Trip can fix the warp engine with "duct tape and a pocket knife". Whether duct tape still exists in the 22nd century or has merely become a proverbial phrase isn't revealed.
- Get Out!: Phlox quickly shoos Organian Malcolm out of sickbay when he begins pestering him with questions about Trip and Hoshi's condition.
- Good with Numbers: Hoshi is revealed to be as good at math as she is with languages, being able to hack well even while delirious.
- I Don't Think That's Such a Good Idea: The alien possessing Malcolm is a bit unsure about it and the alien possessing Travis moving to new hosts, since he fears it'll lead to them influencing the crew and therefore breaking the non-interference policy. Eventually, however, both do so anyway.
- Incurable Cough of Death: The first sign that one's hours are numbered is when the infected person starts coughing. Both of the victims cough, although Trip gets a much nastier cough.
- Instant Sedation: Lampshaded—Phlox tells Trip that he'd better lie down after injecting himself with a hypospray sedative.
- Laser-Guided Amnesia: The Organians utilize this to keep their presence a secret.
- Late-Arrival Spoiler: The Organians being the observing aliens was the big twist at the time, but as you can see here, no one's shy about mentioning it.
- Not So Similar: Archer references the events of "Dear Doctor" when talking about non-interference, but he tells Organian Hoshi that this situation involves a virus that the crew could've been warned about instead of a result of long-term species evolution.
- Oh, Crap!: After Trip flatlines, Archer is quite surprised when "Trip" suddenly begins talking to him. He also backs away in surprise when "Hoshi" suddenly sits up.
- Only Mostly Dead: Trip and Hoshi both get better despite apparently dying.
- O.O.C. Is Serious Business: Trip is a lot more negative than he usually is, believing that he will definitely die, and his reason for the negativity is because he has a silicon-based virus.
- Plague Episode: Discussed. The virus keeps threatening to spread to the rest of the crew, and the aliens keep discussing other times the same illness infected whole crews, but it doesn't become a plague here, since the only characters to get sick are Trip, Hoshi, and briefly Archer.
- Playing Sick: Downplayed— the possessed Malcolm pretends to have a headache in order to speak to Phlox.
- "The Reason You Suck" Speech: Archer calls out the Organians for no longer caring about what happens to the corporeal lifeforms they observe.
- The Reveal: It's clear immediately that aliens are observing the crew and possessing different characters (mainly Malcolm and Travis). That they're Organians is the real twist.
- Shout-Out: The Andromeda Strain really exists.
- Shut Up, Hannibal!: One Organian explains to Archer how advanced their species is. Given that they make a habit of watching, apathetically, while hundreds of species die from an incurable silicon-based virus, Archer snaps back with this:Archer: Not from where I'm standing.
- Sick Episode: Trip and Hoshi are both struck with a silicon-based virus that leaves them delirious for most of the episode. Archer briefly catches it too, but is quickly cured.
- Take a Third Option: Faced with either leaving Trip and Hoshi dead and letting Archer succumb as well or curing them and making their presence known, the Organians cure them and wipe their memories of what happened, leaving them alive and confused.
- Too Dumb to Live: Apparently, sifting through the garbage dump on the planet without wearing any kind of bio-hazard protection gear is a common practice for visitors to the planet. Trip and Hoshi were in their normal uniforms and extremely filthy, making it amazing that they thought they wouldn't contract some kind of infection!
- Undying Loyalty: Discussed when the possessed Travis thinks that the reason Archer is keeping the sick Trip and Hoshi aboard is because Archer is dedicated to his whole crew.
- Unexplained Recovery: Trip and Hoshi, from our heroes' perspective. Thanks to a little Laser-Guided Amnesia, Archer doesn't remember persuading the Organians to bring them back to life.
- Vomit Discretion Shot: When Hoshi throws up, she runs offscreen to do so.
- What Is This Feeling?: When the aliens possess Trip and Hoshi, they talk about how they're now in pain and that pain feels strange and unpleasant.
- You Are in Command Now: Archer tells T'Pol this while he's stuck in Sickbay with dead Hoshi, dying Trip, and his own life in jeopardy.