Enterprise beings with a pan of the ship with eerie music showing nobody aboard, then the music lightens as we see Porthos running around and Phlox chasing after him.  Porthos leads Phlox to where Archer is in a comatose state with a little device on his forehead.

After the commercial break, Phlox is beginning a letter to a colleague to explain to the viewers why everyone is sleeping.  We are taken to a flashback that shows that Enterprise was going to enter a region of space that was going to kill everyone unless Phlox put everyone into comas while they pass through it. 

Phlox is immune to the effects of this special region so he stays awake, he gets a crash course in how to fly the ship

Back in the present Phlox finishes up his letter saying that he’s much looking forward to when he can wake everyone up, but things seem to be going wrong.  Phlox starts hearing things.  He hears what he thinks to be a voice but can’t find it, then a couple of scenes show Phlox singing while he runs around the ship and then feeding his pets in the nude, and then watching a Danny Kaye movie (The Court Jester from 1955).

This particular part of the movie involves an obsessively long tongue twister that is sure to drive anyone out of his or her mind. 

Hawkins: I've got it! I've got it! The pellet with the poison's in the vessel with the pestle; the chalice from the palace has the brew that is true! Right?
Griselda: Right. But there's been a change: they broke the chalice from the palace!
Hawkins: They broke the chalice from the palace?
Griselda: And replaced it with a flagon.
Hawkins: A flagon...?
Griselda: With the figure of a dragon.
Hawkins: Flagon with a dragon.
Griselda: Right.
Hawkins: But did you put the pellet with the poison in the vessel with the pestle?
Griselda: No! The pellet with the poison's in the flagon with the dragon! The vessel with the pestle has the brew that is true!
Hawkins: The pellet with the poison's in the flagon with the dragon; the vessel with the pestle has the brew that is true.
Griselda: Just remember that.

Phlox hears something and goes skulking around the ship to find out what’s going on, where he runs into T’Pol running a diagnostic that is causing gas to be vented in the room that they were in. 

Phlox asks T’Pol what she has been up to over the past 2 days and then asks her to join him in watching the rest of the movie, to which she refuses.  He asks her if she will join him for a meal at some point and she shrugs him off.

Shortly thereafter Phlox hears noises in Engineering and calls T’Pol to ask her what she was doing in Engineering, to which she replies that she was on the Bridge. 

In the galley, Phlox creates a meal for him and T’Pol.  T’Pol asks him what HE was doing in engineering because she was supposed to be maintaining the engines.  He comments on assisting her and then again mentions that he was sure someone was there with him.

While checking on the Captain Phlox sees something "crawling on the hull outside of the ship."  After checking all sensors, T’Pol assures Phlox that there was nothing there.  Then while checking on Hoshi he saw a Xindi Insectoid which then chases him into an airlock.  He then tries to convince T’Pol that it was true and tries to give her a phase pistol but she doesn’t take it, he comments about it being up to them to save the ship and then goes off to find the Xindi.

Walking through the ship T’Pol is counteracting everything Phlox is saying about finding the Xindi, he finds a bio sign on his sensors.  He rounds a corner and fires, barely missing poor Porthos.  T’Pol again rebukes him saying he’s seeing things.

Phlox keeps looking for the Xindi but gets a call asking for help from Hoshi.  He goes to Hoshi, who is in the shower, she comes out of the shower with a cracked face complaining about him doing this to her, the Dieing Sato vanishes and he sees the normal sleeping Hoshi in her bed.  He calls for T’Pol and asks her to join him in sickbay.  On the way he runs into Archer who said that T’Pol woke him up and that he should get some sleep, T’Pol comes up behind him and he turns, when he turns back Archer is gone. 

In sickbay, he confirms that the effect the region of space was having on him was more than he anticipated and that he was indeed hallucinating.  He says he’s going to put himself under and leave the ship to T’Pol but she says that the area of space is affecting her as well, that she can’t control her emotions, and that she needs Phlox there too.

On the Bridge, they are happy that they are about to leave the region and Phlox activates the viewscreen, but what is this?  They are still in it.  He runs long-range sensors where it says that they still have a quarter light-year to go and that at their current speed, it would take another 10 weeks to get out.

They decide to go to warp, Phlox asks T’Pol to activate the warp drive, T’Pol says she can’t and that Phlox should read the manual.  Phlox does and they try to activate the drive and have problems.  This is quite interesting as Phlox gives T’Pol commands on how to activate the core and she feigns inability to do any of it.

After a rocky start, Phlox gets the warp drive started and takes the ship to warp.  We next see Phlox waking Archer.  T’Pol offers to help Phlox wake the crew but he orders her to get some rest instead.  Phlox offers to walk her to her quarters.  When he does he’s shocked to see T’Pol unconscious on her bed.  He had been alone the entire time. 

The episode ends with Phlox speaking to T’Pol in the mess hall, she comments that Commander Tucker said that it would take him weeks to repair the engines but that Phlox "did a hell of a job."  T’Pol mentions that Phlox must have enjoyed having the ship to himself, and he comments that it wasn’t nearly as empty as he thought.