The Enterprise crew is in the process of deploying the second in a series of subspace amplifiers that will allow better communications with home, when an unidentified ship drops out of warp. Captain Archer hails the vessel, but it ominously refuses to respond and just warps away. T'Pol dismisses the "silent treatment" by stating that not every species has motives that can be understood in human terms. So Archer turns his attention to a more pressing concern — doing something special for Lt. Malcolm Reed's upcoming birthday. Archer breaks in the new subspace amplifiers by calling Reed's parents on Earth in hopes of learning his favorite food. He's a bit surprised to learn during the awkward conversation that the lieutenant's own parents don't know what he likes to eat. So the captain gives a reluctant Ensign Hoshi Sato the "mission" of discovering this bit of information about Reed in time for his birthday.
Without warning the alien ship returns, scans Enterprise, fires weapons and immediately goes to warp again. No one is hurt, but the ship barely escaped serious damage. His frustration growing, Archer wonders aloud to T'Pol why there are so many hostile aliens in deep space. He decides to return Enterprise home so it can be fitted with phase cannons, which were never installed because the ship left spacedock prematurely. Reed and Commander Tucker object, insisting that their own crew can build the phase cannons as proficiently as the engineers at Jupiter Station. But Archer orders the ship to turn around anyway. In the meantime, though, Reed and Tucker are granted permission to get the prototype cannon already on the ship up and running, and build two more from scratch, so they put their team on double shifts to try to finish the job en route.
Meanwhile, Hoshi pursues her "secret mission" by speaking with Reed's best friend, his sister and various other relatives, all to no avail. Heeding T'Pol's suggestion to take a more direct approach, Hoshi sits with Reed in the Mess Hall and casually prompts him for what he likes to eat — causing Reed to think she's asking him for a date. Hoshi retracts in embarrassment, but it's quickly forgotten as the "shadow" ship arrives again and attacks, this time knocking out warp drive, main power and tactical systems. Now that Enterprise is adrift, a shuttle emerges from the alien ship and docks itself in Launch Bay 2. Two bizarre-looking spindly aliens board the ship and roam its corridors. Archer leads a couple of security guards to investigate, and they find the aliens standing over two paralyzed crew members, invading their bodies with some kind of energy emanating from their hands. Archer fires his phase-pistol at an alien twice, but it appears to have a shield around its body that absorbs the beams. The aliens walk away impassively, and the guards pursue while Archer contacts Sickbay. But the invaders quickly leave the ship, and when their shuttle docks with its mothership, the aliens fire again and jump to warp. This time they damage Enterprise's port nacelle and cause it to vent plasma.
As Dr. Phlox stabilizes the victimized crewmen in sickbay, Archer realizes they are overpowered by the aliens and need help. Reluctantly, Archer orders Hoshi to contact the Vulcan High Command for help, but then learns that both of their subspace amplifiers have been destroyed, effectively cutting off all communications. Tensions run high as the crew scrambles to restore impulse power and then warp, and also to arm the phase cannons. Reed convinces Tucker that drawing power from the impulse engines for the cannons is an acceptable risk, and the ship prepares to test the new weapons on a nearby moon. During the test a massive unexpected power surge destroys a huge chunk of the moon and overloads the relays on several decks. Investigating the cause of the surge, the crew discovers a strange device installed in the launch bay where the aliens boarded. Scanning it, T'Pol discovers the device is not only responsible for the surge, but has tapped into every system onboard to effectively "spy" on the ship. Archer therefore speaks into a visual interface, assuming the aliens can see him, and angrily announces that humans don't give up easily. Then he destroys the device.
While things are quiet, Hoshi visits Dr. Phlox, still trying to glean Reed's favorite food. Phlox recalls from Reed's medical records that he has been taking regular injections to counter an allergy to bromelin, a plant enzyme found in, among other things, pineapple. That's all she needs. Soon after, the alien ship comes back and sends a transmission: they have taken Archer's visual message to them and re-constructed it to state, "You are defenseless... prepare to surrender your vessel." Enraged, Archer orders Reed to fire both forward phase cannons. He does, but the alien ship's shields completely deflect the energy beams. Remembering the massive firepower from the former power surge, Archer orders Reed to recreate the surge and fire on the ship again, despite the damage it will cause to Enterprise. He does, and the resulting blast disables the aliens' shielding. Reed immediately fires two spatial torpedoes, which punch a significant hole in their ship. As it vents plasma, the alien ship turns and leaves. Confident their foe has retreated for good, Archer decides not to resume course for home.
As Reed, Tucker and the captain celebrate their victory over drinks in the Armory, Hoshi interrupts to present Malcolm with a birthday cake. Malcolm cuts into the cake and, realizing it's pineapple, wonders how on Earth they knew that was his favorite.