En route to Azati Prime, Archer and his crew encounter another roadblock: a trans-dimensional disturbance. To pass through it could prove deadly for the crew, but going around it means another two-week delay. Luckily, Phlox has a solution. He will place each crewmember in a comatose state, so as to protect their neocortexes while they traverse the anomaly. Because Phlox's Denobulan physiology is immune to the effects of the disturbance, he plans to remain conscious and watch over the ship and crew. As there's no way of knowing what effects the disturbance will have on Enterprise's warp drive, Trip recommends leaving the ship at impulse, meaning Phlox will have to keep the crew sedated for at least four days. Phlox is briefed on how to perform various tasks in case of an emergency — Mayweather gives him a quick helm tutorial while Trip instructs him on checking the warp engines. Various crewmembers express their concern about Phlox running the ship, because he lacks Starfleet training, but Archer is confident the doctor can handle things.
After Phlox renders the crew unconscious, he enjoys wandering the halls of the silent ship, taking the time to go for walks with Porthos and write a letter to his good friend Dr. Lucas. Still, the doctor can't help but find his circumstances a bit eerie and isolating. This feeling is compounded when he starts to hear strange noises. While trying to determine the source of the noises, he runs into T'Pol. Apparently, Vulcans are immune to the disturbance's effects as well. T'Pol has been enjoying the solitude of their current situation, but Phlox needs social interaction, so T'Pol agrees to spend more time with him.
As time progresses, Phlox continues to hear strange noises throughout the ship. T'Pol, however, thinks he's just imagining things. But then, during his rounds, Phlox hears noises coming from Hoshi's quarters. Inside, he witnesses a gruesome sight: a Xindi-Insectoid lurking menacingly over the comatose Hoshi. Phlox bolts and manages to escape the Insectoid, but he insists on searching every level of the ship to find the intruders. T'Pol is still skeptical and believes the doctor may just be in need of sleep.
Still, Phlox continues to have disturbing experiences. At one point, he hears Hoshi over the com and races to her quarters. The ensign appears to be disintegrating before his eyes, but a few minutes later, the horrific vision is gone. Hoshi is safely incapacitated in her bunk. Realizing that the disturbance is affecting him as well, Phlox asks T'Pol to put him into a coma until they've cleared the area. T'Pol, however, has disturbing news of her own: she's started to feel as if she's losing control of her emotions, which means the disturbance is affecting her as well. It appears that they will both have to remain conscious.
Then, Phlox and T'Pol make another frightening discovery: apparently, the reconfigured area of space has expanded and Enterprise won't be able to clear it in time. T'Pol and Phlox decide that they must take the ship to warp, despite the danger. The duo heads down to Engineering, but T'Pol is finding it difficult to focus and doesn't seem to remember anything about the warp engines. With help from the ship's database, Phlox manages to successfully take the ship to warp and Enterprise clears the disturbance.
As he awakens the crew, Phlox makes one final startling discovery: T'Pol has been in a comatose state this whole time, along with the rest of the crew. Apparently, she was one of his hallucinations — and oddly enough, one Phlox is very grateful for.