Enterprise is attacked by an unknown alien starship, as Captain Archer orders the crew to install experimental "phase cannons." Meanwhile, Ensign Sato is asked to find out what Lieutenant Reed's favorite food is for a birthday dinner.
In September 2151, while deploying subspace amplifiers to improve their ability to communicate with Starfleet, Enterprise is approached by an alien vessel. Captain Archer hails them, but the vessel returns to warp. He wonders why: Ensign Sato points out that the Universal Translator is far from perfect; and Sub-Commander T'Pol says that some species cannot be understood in human terms. Soon, however, the mysterious ship returns and scans the Earth ship, sending a high pitched screech through the com systems, and firing on Enterprise before again jumping to warp.
Archer notes that Enterprise is now encountering more aggressive species than anticipated, and sets course for Earth so that Jupiter Station can finish the weapons refit. Commander Tucker and Reed ask to be allowed to complete the work themselves, but Archer disagrees, though he gives them permission to begin the procedure. While doing so, the alien ship returns and disables Enterprise's warp drive and main power. Strange alien bipeds then board the ship, and assault two crew-members. They return to their ship, damaging a warp nacelle before departing again. 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, which produces a blast yield 10 times the expected output, due to an unexpected surge. T'Pol traces the anomalous reading to Launch Bay 2, to a device tapped into internal sensors and comm channels. Archer then sends the aliens a message: he does not want a fight but will protect his ship by any means necessary. With that, he destroys the device. T'Pol detects the alien vessel again, which use a re-edited version of Archer's earlier message to demand surrender. 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.