Enterprise is attacked by an unknown alien starship, as Captain Jonathan Archer orders the crew to install experimental "phase cannons." Meanwhile, Ensign Hoshi Sato is ordered to find out what Lieutenant Malcolm Reed's favorite food is for a birthday dinner.
While deploying subspace amplifiers to improve their ability to communicate with Starfleet, Enterprise is approached by an unknown vessel. Archer hails them, but the alien vessel returns to warp. Archer wonders why and Sato points out that the Universal Translator is far from perfect; T'Pol says that some species have motives that cannot be understood in human terms. Ensign Travis Mayweather guesses the aliens did not find Enterprise very interesting.
The mysterious alien ship returns, ignoring Archer's attempt to communicate. They scan the Earth ship and send a high pitched screech through the com systems, disorienting the crew as the aliens fires on Enterprise before jumping to warp. Archer notes that Enterprise is encountering more aggressive species than they anticipated, and because Enterprise left space dock early they did not fit the ship with phase cannons. Archer sets course for Earth so that Jupiter Station can finish the weapons refit. Reed and Tucker plead with the captain to be allowed to complete the work before they get home, but Archer disagrees, though he gives them permission to begin the procedure.
T'Pol detects the alien vessel pursuing them. The vessel disables Enterprise 's warp drive and main power, and a shuttle approaches from the alien vessel. The doors to Launch Bay 2 open and T'Pol cannot reseal them. Two crewmen see alien bipeds traversing a corridor. They follow and Archer sees the aliens standing over the unconscious crewmen, probing them. Archer warns the aliens off, then shoots one of them, with no apparent effect. The aliens return to their ship, which then damages a warp nacelle as it departs, which will take two days to repair. Mayweather suggests contacting the Vulcan High Command for help, but both subspace amplifiers have been destroyed.
Two days later, Enterprise locates an uninhabited planet for a weapons test, and Reed's shot produces a blast yield ten times the expected output, due to an accidental overload. T'Pol detects an anomalous reading in Launch Bay 2. T'Pol reports that a device is tapped into internal sensors and comm channels. Archer activates a view-screen and gives the aliens a message: he does not want a fight but will protect his ship by any means necessary. With that, he phasers the device. T'Pol detects the alien vessel again, which use a reedited version of Archer's earlier message to demand surrender. Archer orders Reed to fire but the blasts barely scratch the alien shields. Archer asks if Reed can intentionally repeat the previous overload of the cannons. Reed complies and damages the alien vessel, knocking out their shields. Reed follows up with two torpedoes before the aliens go to warp.