Two days ago, the Enterprise discovered the formation, which is a "trans-dimensional disturbance". It's right in the way of where they want to go, so to avoid a detour, Phlox had to render everyone else unconscious and fly through at impulse speed lest using warp speed in the disturbance backfire.
Back in the present, Phlox, who is checking up on Travis, continues his letter, revealing that he's taking care of everyone else since his alien physiology made him immune to the disturbance. He also had basic training in helm and engineering, meaning that he can sub for Travis and the engineers. In engineering, he hears a strange noise, but doesn't find anything.
Phlox then takes a jog in the corridor while singing, then feeds his pets in the nude. That night, he watches a movie in the mess hall, then hears another sound. He and Porthos wander into the corridor to investigate the sound, which Phlox tracks to the launch bay. He sees a gas leak rattling a chain, causing him to quip to T'Pol who just appeared about living in a haunted house. He asks her to dinner, and she accepts. Later, Phlox does a maintenance check in engineering when he sees a shadowy figure running. He thinks it's T'Pol and angrily tells her off on the intercom, but she claims to be on the bridge.
At dinner, Phlox tells T'Pol, who doesn't have an appetite, that his species enjoy crowds and he hates being alone. He goes back to sickbay and continues his letter, then checks on Archer, only to see another shadowy figure outside the window.
He calls T'Pol, who tells him in the situation that there are no lifeforms nearby, but Phlox is unconvinced. He finds a Xindi-Insectoid inside Hoshi's quarters, who (along with a second Xindi-Insectoid) chases him around and into the airlock. From there, he tells T'Pol that there are Xindi onboard. He tells her about the incident in the armory, but she's very doubtful and doesn't accept a phase pistol that Phlox offers her. Phlox takes his own phase pistol and decides to search the ship.
T'Pol reluctantly agrees to help him search, and as they search, Phlox nearly shoots Porthos by accident. This causes an argument, with T'Pol getting uncharacteristically angry, and they separate. Phlox hears Hoshi calling and when he arrives at her quarters, he sees her emerge from the shower with a disfigured face. She blames him for "letting" her get the severe injuries, but when Phlox exits the bathroom, he sees Hoshi unconscious on her bed and the shower off.
Realising that he's probably seeing things, Phlox decides to go to sickbay, and on the way there, he sees Archer in the turbolift. However, this turns out to be another hallucination when "Archer" is nonchalant about the idea of Xindi outside the ship. Phlox scans his brain and notifies T'Pol that he has been hallucinating, and offers her to take over. She refuses, claiming that the disturbance is giving her mood swings. On the bridge, they discover that it's going to take them longer than they thought to get out of the disturbance— ten weeks in fact.
They discuss the situation and T'Pol suggests that they regain warp drive, but in engineering, she's too distracted to help. Phlox hallucinates Trip reminding him not to go into warp, and when they continue to have trouble, T'Pol suggests waking up the real Trip, despite the fact that he'd die if exposed to the disturbance. Finally, Phlox manages to get the ship to fly at warp two.
The ship gets out of the disturbance and Phlox awakens Archer and a hungry Trip. He then enters T'Pol's quarters and finds out that she was also unconscious the whole time and all the interactions he had with her were hallucinations. He decides to send Dr. Lucas the delusional letter anyway because he might be entertained by it. As life on Enterprise goes back to normal, Phlox dines with T'Pol, for real this time.
Tropes in this episode include:
- All Just a Dream: Turns out T'Pol was asleep the entire episode. The rest of it wasn't.
- Artistic License – Gun Safety: Phlox points the phase pistol at his own head. Understandable, though, given what he's going through at that moment.
- Body Horror: Phlox has a hallucination of a badly disfigured Hoshi.
- Bottle Episode: Shot only on the ship sets and featuring absolutely no guest stars.
- Call-Back: In "Exile," Phlox told Hoshi that Denobulans consider it healthy to hallucinate when under stress and that he envied those who could do so. Still think that way, Phlox? It also serves as a hint that T'Pol is not real, as there is absolutely no reason she should be aware of this conversation.
- Captain's Log: With Archer asleep for the episode, we instead get a letter from Phlox to Dr. Lucas explaining How We Got Here.
- Dare to Be Badass: With T'Pol's encouragement, Phlox manages to start up the warp drive on his own.
- A Day in the Limelight: Phlox is the main character in this episode.
- Didn't See That Coming:
- Phlox realizes that he was so busy tending to the comatose crew that it never occurred to him to scan himself for how the transdimensional disturbance could be affecting his mind.
- The crew knew the disturbance would expand, but it accelerated far faster than expected.
- The Ending Changes Everything: Watching the episode again will reveal all the clues that T’Pol was a hallucination the whole time, such as not eating the dinner that Phlox had prepared and not being helpful at all while restarting the warp reactor. This is even Lampshaded when Phlox considers deleting what is now a largely fictitious account of the experience, but decides that Lucas might find it entertaining.
- Evil-Detecting Dog: Inverted. Porthos never reacts to anything Phlox sees or hears. Considering that dogs would likely hear better than any non-Ferengi humanoids, this is the first clue that everything is in Phlox's imagination.
- Friend or Foe?: Dr. Phlox mistakes Porthos for an intruder because he failed to set his handheld scanner to differentiate between canines and Xindi. Dr. Phlox shoots at and barely misses the poor bewildered dog.
- Foreshadowing: More talk of a transdimensional region rewriting areas of space.
- Gallows Humor: As always, Phlox has a cheerful attitude over having to watch the entire ship by himself.Trip: If the impulse manifolds get clogged, the engines'll overload. That would be very bad.
Phlox: I imagine it would. - The Ghost: Phlox mentions he'll be awakening his medical staff soon. A medical staff we have never seen, outside of emergencies and whoever happened to be in sickbay.
- Go Mad from the Isolation: The episode, showing what happens when Denobulans are deprived of interpersonal interactions for more than a couple days — they hallucinate.
- Hard-Work Montage: Phlox learning how to operate Enterprise by himself.
- "Hell, Yes!" Moment: Phlox successfully getting Enterprise to warp 2, despite having little understanding of warp mechanics and a tenuous hold on what's left of his sanity.
- I'm a Doctor, Not a Placeholder: Phlox is a physician, not an engineer.
- In Medias Res: The episode opens with Phlox chasing Porthos through a deserted Enterprise.
- Moving the Goalposts: The anomaly suddenly expands much faster than expected, no doubt thanks to the Sphere Builders.
- Naked People Are Funny: One gag involves Phlox, naked, feeding his pets in sickbay.
- The Needs of the Many: Trip tells Phlox to wake him if things get really sticky, even though it will kill him. Phlox, however, isn't so willing to sacrifice him.
- Not So Stoic: Despite being a Vulcan, T'Pol (perhaps because she's just a hallucination) argues with Phlox when he nearly (accidentally) shoots Porthos.
- Oh, Crap!: Phlox spends much of the episode in this state, but it really hits the fan when he finds out the disturbance's expansion has accelerated and that it will take ten weeks to escape at impulse.
- Out-of-Character Alert: T’Pol losing her train of thought and being of no help when Phlox tries to restart the engines are clues that she isn’t real.
- Pet the Dog: Phlox lets Porthos have one of his alien leeches as a snack. "Don't tell the Captain."
- Primal Fear: Complete isolation is this for Denobulans (whose culture includes communal lifestyles and large extended families).
- Read the Freaking Manual: Phlox wails this trope practically by name before diving into the impenetrable block of technobabble that is the warp drive guide.
- "The Reason You Suck" Speech: Hallucination!Trip telling Phlox that he's gonna screw everything up.
- The Reveal: At the end of the episode, Phlox walks T'Pol back to her quarters...and finds her still asleep.
- Scenery Censor: Phlox shows up one morning in sickbay completely naked. Thankfully, his animal cages and a large tablet conceal his private parts.
- Shoot the Dog: Phlox almost literally does this to Porthos when he thinks a Xindi is coming from around a corner.
- Shout-Out:
- When trying to stop Porthos from running, Phlox shouts "Return!" as if he were a Pokémon trainer.
- The movie that Phlox watches is The Court Jester.
- Phlox also mentions Tucker showing him The Exorcist.
- Phlox seeing something outside the window and T'Pol not believing him comes off as very similar to the classic Twilight Zone episode "Nightmare at 20,000 Feet." Given said episode starred an actor made famous in the original series, it's likely intentional.
- Techno Babble: Phlox is utterly baffled by the engineering manuals, saying that they may as well be written in ancient Klingon.
- Why Did It Have to Be Snakes?: Denobulans love crowds and socialization, so being the only conscious crewmember on the ship would be a miserable experience for Phlox in the best of circumstances.
- You Are in Command Now: Due to necessity, Phlox is given tutorials in everything from helm control to engineering since he's the only person who can survive the anomaly awake.
