As Captain Archer prepares to lead a survey team to an uninhabited planet, Enterprise is suddenly hailed by a trio of aliens seeking refuge. The aliens warn Archer that a deadly neutronic wavefront is quickly approaching. After conferring with the crew, Archer surmises that everyone must take shelter somewhere protected in order to survive the storm's deadly radiation. Trip suggests that the one heavily-shielded place onboard that might suffice for the eight-day ordeal is the cramped quarters of the catwalk, the maintenance shaft that runs the length of each nacelle. Only one problem — the temperature in the catwalk can reach 300 degrees when the warp coils are online, so Trip will have to shut down the main reactor and set up a makeshift bridge in one of the catwalk compartments.
The crew and their alien visitors evacuate to the catwalk, and as the days wear on, tensions run high among them. The storm envelops the ship, making for frequent, sudden bouts of turbulence. Also, the alien trio doesn't do much to endear themselves to the Enterprise crew, and even endangers the crew by trying to cook their food near a plasma manifold. To make matters worse, Trip and Archer discover a problem in Engineering — the matter and antimatter injectors have come online, endangering the crew's safe haven in the catwalk. Trip cannot shut the injectors down from the catwalk, however — outfitted in an EV suit, he must make the trek to Engineering. The suit will only protect him for 22 minutes, so he has to work fast.
Once Trip reaches Engineering, he notices something even more peculiar — alien intruders, who appear to be interfering with the ship's systems. Trip manages to hide from them, and attempts to ascertain what they're doing aboard Enterprise. As he peers out a window, he notices an alien ship docked alongside Enterprise. He also manages to activate a monitor and witnesses the aliens on the bridge — oddly enough, they're the same species as the trio of aliens taking refuge in the catwalk. Trip returns to the catwalk and relays his findings. Phlox runs a scan on the alien visitors, deducing that the aliens are actually immune to the effects of radiation. Angered, Archer demands to know what's going on. The trio confesses that the aliens Trip saw are actually looking for them — they're considered fugitives. They explain to Archer that they were officers in the Takret Militia, but they escaped when they learned that the commanding officers were corrupt. The trio apologizes for lying to Archer, and tells him that these alien intruders have a history of seizing vessels like Enterprise and murdering the crews.
Reed reports that the alien intruders are trying to re-initialize the warp reactor, putting the crew in danger. Realizing that he must act quickly, Archer formulates a plan. He, T'Pol and Reed suit up and head down to the main area of the ship. While T'Pol and Reed work to shut down the warp reactor, Archer distracts the alien leader, claiming to be the only survivor onboard Enterprise. He demands they leave, or he'll destroy the ship. He then breaks contact, and orders Mayweather to change course, heading straight for a destructive plasma eddy. As T'Pol and Reed finally succeed in shutting the reactor down, the alien leader realizes that Archer is serious, having set Enterprise on a suicide course towards the plasma eddy. He and his men flee the ship, and Mayweather manages to steer clear of the eddy just in time.
Soon after, Mayweather maneuvers Enterprise out of the storm, and the crew is able to return to their quarters. The alien visitors, meanwhile, apologize for all the trouble they've caused, and head for the Gyrannan System. Relieved that the whole ordeal is over, Archer wishes them luck and bids them farewell.