S1:E12: Silent Enemy: Enterprise is confronted and then toyed with by an unknown alien starship, which raises Captain Archer's concerns on Enterprise's readiness for the unknown.
While cruising along, an unknown alien species takes an interest in Enterprise. At first, when they don't respond to hails, Captain Archer & his crew are suspicious of their motives after they leave. However, when they return and shots are fired, the Enterprise crew are made aware of the dangers that exist in the vastness of unexplored space. Technology onboard Enterprise, though thought to be "state of the art" by the crew, are quickly informed that they may not be up to snuff with those whom they may encounter.
The realization that two of their phase cannons weren't installed prior to their maiden voyage to return Klaang to Qo'noS becomes evident when they're unable to properly defend themselves against these hostile enemies. Captain Archer ultimately decides to turn the ship around and return home to have Starfleet properly finish outfitting the Enterprise with all of her intended armaments.
Commander Tucker, Lieutenant Reed, and the combined Engineering and Operations departments work around the clock to complete the upgrades so that as Trip puts it, "By the time we reach Jupiter Station, I don't want their engineers to have a thing to do but give us a wash and a wax."
The B story also centers around Hoshi being given the task of finding out what Malcolm's favorite food is so that Captain Archer can have the chef prepare it as a surprise for Malcolm's birthday. One by one, Hoshi contacts family members, friends and colleagues of Malcolm's who are only able to verify that they once ate something with him. Hilarity also ensues when Malcolm misinterprets her invitation to dinner in her quarters as a romantic proposition.