As Enterprise orbits a nearby planet, it seems that Travis Mayweather and Malcolm Reed are rapidly playing chess on board the ship in the mess hall. In reality, however, they are under the control of two noncorporeal aliens. They talk about the game in technical terms and discuss the Humans they are observing on Enterprise. When “Mayweather” asks “Reed” how the Humans will react to what they find on the planet’s surface, “Reed” answers that, in his experience, at least one member of every species that has come here has died as a result. He also mentions that some species have lost an entire crew.
In a shuttlepod, Trip and Hoshi are returning to Enterprise from the M-class planet, where they were excavating a Klingon garbage site. Tucker hails the starship and speaks with Captain Archer. He tells the captain that their search was unsuccessful. All they found was an old power cell, some empty ration packs and a latrine. Suddenly, Tucker starts coughing uncontrollably and eventually collapses. Sato informs the senior officers of Tucker’s condition. “Mayweather” and “Reed” watch as Archer asks Sato to pilot the shuttlepod into the launch bay and requests that T’Pol notifies Doctor Phlox to be ready.
Archer and Phlox watch Tucker and Sato from outside the decontamination chamber. Archer says that the shuttlepod will have to be inspected to check whether any of its environmental systems were the cause of Tucker’s condition. Phlox tells Sato that three landing parties have returned to Enterprise with no ill effects and passes medkits to them through an opening in the bulkhead. He requires samples of their blood which he can then begin to analyze. Sato starts to cough and recalls that Tucker started coughing shortly before he lost consciousness. Phlox tells his two patients to get him their blood samples as soon as possible and leaves with Archer. As he and the captain walk through a corridor that leads away from decon, he informs Archer that he’s having difficulty determining the cause of their infection using standard scans.
In another corridor, “Mayweather” mentions that he studied “Reed”‘s report on how the Klingons dealt with the infection, to which “Reed” answers that they responded typically for a species at their level of development. When “Mayweather” comments that he believes Archer and the Klingon commander acted differently, “Reed” disagrees. “Mayweather” argues that the Klingon commander didn’t allow his landing party to beam back on to their ship, although Archer did. In response, “Reed” explains that both courses of action were extremely similar – the areas of the ship that Tucker and Sato have visited since their return, the launch bay and the decon chamber, are completely isolated from the rest of the starship. He claims that it doesn’t matter if a member of the landing party returns to their vessel and that the aliens learned everything they can from humans. “Mayweather” remembers that, like the humans, the Cardassians were also concerned for each other. However, “Reed”‘s response is that the Cardassians eventually killed the infected members of their crew, as did the Klingons, if not quite so rapidly. Although “Mayweather” seems hopeful that the Humans may overcome the virus, “Reed” answers that he’s been observing aliens for eight hundred years and hasn’t been surprised yet. Their protocol dictates that they should question the infected crew.
In decon, Tucker looks over the temporary medication which the doctor has provided, to be used for muscle pain and nausea. There is also a cough suppressant but Sato comments that they aren’t coughing any more. She thinks that could be because they’re slowly recovering. Trip reminds her that Phlox issued the medication, which he feels is an adequate reason to take them. “Mayweather” arrives at decontamination and asks what’s in the hypospray. Trip explains that Phlox has been unable to make a diagnosis. “Mayweather” continues to question them, asking if they’ve ever faced serious illness before and how their present condition compares with any other illness they may have experienced. Trip gradually gets annoyed by the entity’s questions and eventually closes the hatch that allowed “Mayweather” to observe.
In sickbay, Phlox is analyzing Sato’s and Tucker’s blood samples when “Reed” enters. He claims he has a headache, so the doctor tries to find some relevant medication. “Reed” is interested in the computer displays of Sato and Tucker’s blood. Phlox returns and scans “Reed”, determining that the headache is not serious. “Reed” explains that it could get worse, though, so Phlox administers him with a mild analgesic. “Reed” asks the doctor how he plans to create an effective antidote but when Phlox begins to believe that “Reed” is afraid that the virus is contagious, he shows him the door.
In decon, Tucker asks Sato if she has ever seen a movie from the 20th century entitled, The Andromeda Strain. Unaware of the film’s premise, the semi-delirious Sato guesses that it is about a Doctor Andromeda who builds a monster which eventually kills him. When Tucker tells her that the film actually involves an alien virus, she replies that she finds it hard to differentiate between the plots of the many films that Tucker likes, due to their extreme similarities. Tucker recalls that he “got into a lot of trouble” at Starfleet Training Command and Sato confesses that she was dismissed from Starfleet. She recalls that when she was trying to run a poker game for some of the new recruits and several members of the training staff stationed there, a company commander attempted to terminate the game by sweeping the chips off the table. As a result, Sato, an experienced student of aikido, broke the commander’s arm. Tucker wonders how she managed to be assigned to Enterprise following the incident, to which Sato replies that Starfleet was desperate for language specialists and that she was reassigned on probation.
In sickbay, Phlox tells Archer that Sato and Tucker are suffering from a silicon-based virus. Archer wonders how the virus could have evolved on an M-class planet, where only carbon-based life is known to exist. Phlox theorizes that it may have traveled to the planet on the surface of a meteorite, which could explain why only one of the four landing parties sent by Enterprise contracted it. He informs Archer that there is no record of the virus in the Denobulan medical database, so he’ll have to work without prior research. He says that the pathogen is reproducing at an incredibly fast rate and that if he cannot find an antidote, Sato and Tucker may only have five hours to live.
As Enterprise continues its orbit of the planet, “Mayweather” and “Reed” discuss their observations of the crew in the mess hall. “Mayweather” tells “Reed” that Phlox has managed to make a diagnosis and that no one on board has made the decision to abandon the infected members of the crew. “Reed” believes that everyone aboard the ship will die as a result.
Archer arrives outside the decon chamber and tries to open the observation hatch. Trip thinks that “Mayweather” has returned but is relieved to find instead that his visitor is Archer. He tells the captain that Sato is asleep and that the medication which Phlox gave them seems to be working. Archer informs him that the doctor has identified the pathogen but has so far been unsuccessful in creating an antidote. When Tucker begins to speak pessimistically about the amount of time he has left to live, Archer tells him that his immune system could still reject the virus. Trip recalls that, due to their carbon-based nature, Human bodies don’t repel silicon, which he learned from Exobiology 101. When Archer advises him not to give up, Tucker seems optimistic about exploring new worlds. Deeply saddened by the engineer‘s ill health, the captain asks him to rest.
As they walk through a corridor, “Mayweather” and “Reed” agree that they are searching for indications of advanced rational intelligence within the species which they observe. However, “Reed” remarks that Captain Archer hasn’t shown signs of rational intellect. By allowing Sato and Tucker to remain on board, he has increased the possibility that their quarantine may fail. However, “Mayweather” is certain that Archer knows the risk that the virus represents and that perhaps it is not as important to him as being committed to his crew. “Reed” thinks that “Mayweather”‘s suggestion is as probable as the chance that Archer is unaware of how unfortunate the situation has become. So, in order to learn whether Archer realizes the risk of contamination, “Mayweather” suggests that he and “Reed” transfer to new hosts. He elects the bodies of Phlox and T’Pol to be used, since Archer’s decisions are based on their findings. “Reed” responds by reminding “Mayweather” that the noncorporeal beings have a strict non-interference policy and claims that the more hosts they occupy, the greater the chance of accidentally influencing the crew. On the other hand, “Mayweather” states that the more crew members they inhabit, the more they will be able to observe.
In decon, Tucker and Sato discuss Sato’s linguistic capabilities. Tucker reveals that he’s always been jealous of her ability to learn new languages, while Sato claims that she wishes she had Tucker’s skill to repair warp engines with “duct tape and a pocket knife“, as she puts it. He tells her that he hasn’t always been good at construction and gives a humorous example of how he once enjoyed taking things apart. Once he has finished recounting the story, Sato stands up and sees Phlox and T’Pol at the observation window. Unknown to Sato, they are now occupied by the noncorporeal aliens, although both she and Tucker seem surprised at the sight of them. When Tucker asks how their research is progressing, “T’Pol” replies that they are waiting on some new test results and “Phlox” adds that they came to check the condition of their patients. When Tucker asks them to return to sickbay and continue their work, “T’Pol” claims that they intend to immediately do exactly that. “Phlox” is more reluctant to leave than “T’Pol” but eventually does so, too. Sato realizes that “Phlox” and “T’Pol”‘s joint visit could be an indication that they’re almost finished their work in sickbay, though Tucker isn’t as optimistic.
While “Phlox” and “T’Pol” wander through a corridor, “Phlox” comments that Sato and Tucker are very brave in the way they are facing death. “T’Pol” replies that their intelligence is in question, not their courage. When “Phlox” judges that “T’Pol” wants the Humans to fail, she answers that it isn’t a contest. She explains that it is more a question of whether the Humans are sufficiently intelligent for the noncorporeal aliens to initiate first contact with them. “Phlox” suggests that the aliens also consider other qualities in that decision but “T’Pol” clarifies that they have used that characteristic for ten thousand years. She maintains that they aren’t responsible for changing the factor which is used as an indicator but “Phlox” asks who is.
On the bridge, Archer and Reed look over sensor data from the planet below. They have detected a crater, which could prove Phlox’s theory that the virus travelled to the planet on a meteorite. The captain thinks that the crater could be the source of the pathogen. If so, the Klingons who set up the campsite which Tucker and Sato explored would also have been infected. Archer orders Reed to contact Starfleet to find out whether the crew of the Klingon ship which visited this world were able to develop a cure.
In sickbay, the new test results which Phlox is waiting for are ready. “T’Pol” states that the aliens should transfer into new hosts to allow Phlox and T’Pol to continue their work. They agree to re-inhabit the bodies of Reed and Mayweather, who are on the bridge, and soon leave Phlox and T’Pol. With no indication of the alien’s presence, Phlox observes a viewscreen which shows the results of the blood test he performed earlier. He comments that the alterations they made to the blood’s immune receptors weren’t effective. Indicating an area of the viewscreen, T’Pol mentions that it may show evidence that the virus is sensitive to ionizing radiation, however the amount needed to kill the virus would also be lethal to Tucker and Sato. The doctor agrees and, with his encouragement, she begins to prepare new blood samples for testing.
In decon, Sato wakes from a nightmare. She dreamed that she was in Brazil, where, in reality, she taught as a university professor of languages, shortly before her assignment as Enterprise‘s communications officer. In the nightmare, which seemed very real to her, a shuttle was on its way to take her to the ship. Tucker reminds her that she is aboard Enterprise, which seems to calm the ensign. She tells Tucker that she didn’t have enough time to say goodbye to her students but the engineer promises that she will see them again.
On the bridge, Archer informs “Mayweather” and “Reed” that he’s spoken to the members of Starfleet Command, who are working through diplomatic channels to contact the Klingons. However, their communication may be unnecessary, as Archer has found evidence of a Klingon alloy in orbit of the planet. The alloy is used as the Klingons’ standard hull plating and comprises the remains of a Klingon shuttlecraft. Archer has realized that the vessel’s crew, infected with the silicon-based virus, were killed by their commanding officer. “Reed” remembers that the crew “didn’t even plead for mercy” but, when he notices that Archer is watching him, he disguises the recollection as an observation on Klingon honor. When “Mayweather” asks if learning about what happened to the Klingons helps the crew of Enterprise in any way, Archer replies that it would be pointless to ask the Klingons for the cure, since they now know that the Klingons didn’t develop one. He says that he would do anything it took to acquire the antidote if the Klingons had developed it.
In the decon chamber, Sato is desperately trying to escape. She frantically speaks several different languages, including a diverse range of Terran as well as Klingonese. When Tucker tells her that she won’t be able to break the security lock-out code, she answers that “math is just another language”. An alarm klaxon blares, signaling that there is a quarantine breach in their area – Sato has broken the code.
On the bridge, “Reed” reports the breach to Archer and looks at “Mayweather”, surprised by Sato’s actions.
Meanwhile, Sato walks through a corridor outside decon in an extremely delirious state.
Sato opens a door at the other end of the corridor and walks through.
On the bridge, “Reed” informs Archer that the ensign is overriding the safety interlocks on D Deck. The captain orders him to shut down all power on that deck in an attempt to seal every door there.
As Sato tries to break through another door, sections of the corridor behind her darken. Eventually, the entire deck is plunged into darkness and a red emergency light is automatically activated. Tucker appears behind her and tries to persuade her to stop what she’s doing. He tells her that the door which she is attempting to open is actually an airlock. If she succeeds, she and Tucker will die of exposure to space. She replies in Russian, insisting that she must say goodbye to her students before she leaves for Enterprise. When Tucker attempts to hold her back from the airlock, Sato wrestles with him. She is weakened by the virus, however, and doesn’t have enough energy to fight against him for long. Tucker misunderstands her when she says, “I need to tell them… while there’s still time.” He thinks she is speaking about the senior officers when she says “they”, and that she believes she and Tucker will die because of the virus. He reminds her of Archer’s determination and leads her back to the decon chamber, where the alarm ceases to sound. As she rests on one of the bunks there, Tucker contacts sickbay and tells Archer and Phlox that they have returned to quarantine. The doctor instructs Tucker to use a hypospray and inject Sato with three units of sonambutril, an extremely high dosage. The captain adds that the sonambutril will ensure that Sato remains in the decon chamber. Complying with the doctor’s orders, Tucker remarks on Sato’s ability to escape. Once he has injected Sato, Archer tells him to do the same to himself. When he argues with that decision, Phlox explains that the virus is incompatible with carbon-based life and that the Denobulan hasn’t found a method to predict its attack. After some debate, Phlox and Captain Archer persuade Tucker to comply. After injecting the sonambutril, the engineer collapses down onto the other bunk.
In sickbay, Phlox reports that he and T’Pol have managed to isolate a specific frequency of radiation which disrupts the silicon matrix of the virus. However, the dosage of radiation which the potential patient would have to be subjected to would be lethal. Archer thinks that there must be a way to cure the patient without killing them. Phlox agrees and notifies the captain that he is currently working on that. Archer advises him to quicken his research.
On the bridge, “Mayweather” walks to the tactical station and whispers to “Reed” that they should stop the effects of the virus. “Mayweather” recalls that they came to observe the crew’s reaction to the unexpected, not to watch the crew suffer. “Reed” doesn’t recommend their discussion take place on the bridge, so “Mayweather” advises that they speak elsewhere.
In the decon chamber, Sato and Tucker sit straight up as they are occupied by the two non-corporeal aliens. “Tucker” is surprised by how the sensations of his host differ from those of the other crew members. Uncomfortably, the alien comments that he, like “Sato”, is also experiencing physical pain. He wonders why Humans should endure pain, which he regards as a weakness. “Sato” claims that the desire to overcome pain will eventually drive Humans to evolve beyond the limitations of the physical world. “Tucker” hypothesizes that “Sato”‘s argument might not be applicable to every species which they encounter but “Sato” answers that it can at least be applied to their own species.
In sickbay, Phlox is shocked when he sees “Sato” and “Tucker” standing in the decon chamber, talking to each other. He doesn’t suspect their alien influence and is puzzled that they are even awake. For a brief moment, he watches as the aliens discuss the Human and Klingon crews which they have observed. Soon, “Sato” senses that they, too, are being observed and the aliens leave their hosts’ bodies.
When Phlox sees “Archer” and “T’Pol” walk through the doors to sickbay, he expects that they are also their usual selves. He hands “T’Pol” a PADD which shows the brain wave patterns of “Tucker” and “Sato”, surprised that the patterns aren’t Human. When he eventually discovers that Archer and T’Pol are occupied by aliens, Phlox asks whether they are responsible for what happened to Tucker and Sato. “Archer” responds that they are not, and “T’Pol” explains that they are only interested in studying how physical species respond to the unknown. She adds that Phlox could assist the aliens by explaining how he noticed their presence. The doctor tells them that Sato and Tucker were sedated and, therefore, should not have been able to stand or talk. “Archer” tells Phlox that they were unable to distinguish between sleep and sedation, as it had been so long since they had inhabited physical beings. When Phlox asks the aliens if they could help Sato and Tucker, “T’Pol” reminds him of their non-interference protocol. The doctor argues that they are interfering with him, which contradicts their protocol, but “T’Pol” replies that they are observing Humans, not Denobulans. When the alien informs him that they recently occupied his body, Phlox is surprised that he can’t remember that happening but “Archer” tells him of the simplicity of memory adjustment. The doctor believes that since the aliens have the ability to alter Human and Denobulan memories, they must also be able to help Sato and Tucker. “T’Pol” refuses to assist the doctor’s patients and thanks Phlox for his help. He, however, is appalled at the aliens’ actions and isn’t surprised that they erase memories.
Later, “Archer” and “T’Pol” walk through a corridor outside sickbay. “Archer” thinks the Humans may have developed a cure for the virus, but “T’Pol” informs him that she has watched several other species develop the same treatment – although after their patients had died. She tells him that they didn’t initiate first contact procedures with any of those species and that it would be illogical to have done so. Reminding “Archer” that their current hosts are busy members of the crew, she insists that the aliens return to Mayweather and Reed.
As Enterprise continues its orbit of the planet, Phlox and T’Pol report to Captain Archer. Phlox says that if the radiation is to be precise enough as to destroy the virus without killing Sato or Tucker, the bio-scanner in sickbay will have to be used. T’Pol suggests that the quarantined area is expanded in order to accommodate the infected crew members. Determined to help his crew, Archer replies that implementing Phlox and T’Pol’s plan won’t be a problem.
Some time later, Phlox notices Sato’s bio-readings deteriorate. Dressed in environmental suits, he and Archer enter the quarantined area of the ship, as “Mayweather” and “Reed” watch them on a monitor. When they arrive at the decon chamber, the doctor notes that Sato is entering oligemic shock and may soon be dead. Phlox and the captain carry her and Tucker into sickbay, where Archer calls out that Sato isn’t breathing.
Meanwhile, “Reed” repeats several words he said earlier – “someone always dies”.
In sickbay, Phlox and Archer attempt to revive Sato. Just before Phlox removes one of his EV gloves, the captain stops him and asks what he’s doing. The doctor replies that he needs a better grip to operate the medical equipment, so Archer removes his own gloves, saying that a doctor is more urgently required on Enterprise than a captain is. The captain exposes himself to the virus – likely sacrificing his own life – in the hope that the doctor will find the antidote. They prepare the equipment for a cardiopulmonary resuscitation technique.
Meanwhile, “Reed” comments that their behavior is highly unusual. In 800 years, no one else that the aliens have observed have exposed themselves in an attempt to resuscitate their infected crew.
In sickbay, Phlox instructs Archer to inject forty units of trinephedrine into Sato’s heart. Phlox also tries to revive her using electrostimulus, but to no effect. Sato dies on the medical bed. Next, Archer and the doctor try using the radiation treatment to save Tucker.
Outside the quarantine area, “Mayweather” wonders why so many Humans have to die before “Reed” will acknowledge that they are different. “Reed” answers that he will not ignore the aliens’ protocol. He says that the incident which they have been directed to observe isn’t over, and, now that the first death has occurred on the ship, there is a higher chance that the other crew members will become infected. He reminds “Mayweather” that the aliens are not responsible for the virus and that members of the crew would have become infected even if the aliens had not observed the situation. “Mayweather” asks what more can be learned from the Humans and suggests that the aliens should perhaps start to take responsibility for the effects of the virus.
In sickbay, Archer completely covers Sato with a blanket, signifying her passing. The captain then helps Phlox move Tucker into sickbay’s imaging chamber, where they irradiate his body. When they remove him from the chamber, Phlox murmurs that the procedure was ultimately unsuccessful. The doctor says that he did all that he could have done for Tucker, but Archer could still be cured in the few hours he has left to live. The captain orders Phlox to go to the bridge instead, saying that the doctor could be infected if he remains in sickbay. Once Phlox has left, Archer contacts the bridge. He makes sure that T’Pol knows she is now in command of Enterprise and tells her not to let Admiral Gardner place anyone else in command. He also says that if Tucker regains consciousness, he will immediately inform T’Pol and closes the communication channel to the bridge. Placing a hand on Tucker’s chest, he watches a monitor as the engineer’s low bio-signs fall to zero. Like Sato, Tucker also dies of the alien virus.
Archer is startled when the engineer’s body is inhabited by one of the non-corporeal aliens, who tells the captain of the respect the alien has for Archer. When the captain becomes confused at Tucker’s regaining health, the alien tells Archer that the engineer has been inhabited by an Organian, a “nonphysical lifeform”. The Organian explains why the aliens come here and repeats information regarding their non-interference protocol. He tells Archer that he wanted to warn the captain of the silicon-based virus, but that decision was not his to make. When “Sato” sits up and debates with “Tucker” on the subject of the Organians’ directives, Archer interrupts that he doesn’t care about their rules. When he questions them, “Sato” responds that the Organians are instructed to leave their hosts’ bodies as they found them – they will have to leave their current hosts dead. The captain agrees that the decision of whether to become involved with a species’ natural development is a difficult choice but suggests that the aliens could communicate verbally with their subjects, in order to learn more about them. Sato argues that talking is a “limited form of communication” for the Organians, who are much more advanced than that. Archer disagrees, replying that the aliens don’t seem more highly evolved than Humans, due to the fact that they have lost empathy and compassion – characteristics which give life meaning. When “Sato” tells the captain, who is now beginning to exhibit the symptoms of the virus himself, that the Organians will soon leave, erasing his memory of their presence, she informs him that he himself will die in just three hours. However, “Tucker” refuses. When a stunned “Sato” accuses him of insubordination, “Tucker” responds that he’s defying 10,000 years of protocol on alien interaction. He insists that they save the Humans and gives Archer’s compassion as a reason. When “Sato” promises that the aliens will eventually study other Humans, Archer suggests to her that the Organians experience compassion for themselves, in an effort to learn more about what it means to be Human.
On the bridge, Phlox and T’Pol are contacted by Archer. Recalling his promise to let T’Pol know if Tucker ever came to, he tells her to come down to sickbay, where he’s not only awake, but quite talkative – as well as Sato. When Phlox grimly interjects that she’s dead, Archer insists that the doctor come as well, since he might have a better shot at figuring out what just happened.
Later, a baffled Phlox reports that he has detected no sign of the virus in Sato, Tucker, or Archer. He thinks their rejuvenation must have been a delayed result of Tucker’s radiation treatment, although that wouldn’t explain why Archer and Sato are well again. T’Pol suggests that the pathogen’s behavior is more unpredictable than she and the doctor had assumed, which could account for Sato and the captain’s health. Smiling, Archer comments that the virus will later be studied by Starfleet Medical and notifies the crew that he plans to leave a warning beacon in orbit of the planet, to warn visitors of the harmful effects of the virus.
In a turbolift, “Mayweather” is pleased that the Organians will never be able to observe another species encounter the virus and that, after 10,000 years, the aliens’ rules will finally be changing. He informs “Reed” that he plans on advising the other Organians to begin preparations for first contact with Humans, which “Reed” suspects will occur in five thousand years. “Mayweather” tells him that they had better get started.
Finally, Enterprise leaves the planet’s orbit.