"Affliction" is the fifteenth episode of the fourth season of Star Trek: Enterprise and the first episode of a two episode arc.
A Klingon scientist works in a laboratory, watched by a Klingon general and a guard. A representation of a DNA helix is displayed behind the scientist. A door opens and a Klingon prisoner is led into the laboratory by two soldiers of the Empire. In Klingonese, the prisoner claims that his death sentence was commuted and demands to speak with the magistrate who presided over his trial. The Klingon soldiers strap him to a chair and hangs a vial of green liquid above his head, which the scientist injects him with. Confused, the prisoner wails as his cranial ridges ripple and begin to dissolve.
Returning to Earth, Enterprise finds the NX-class starship Columbia in an orbital drydock facility, undergoing final preparations for her maiden voyage.
Doctor Phlox and Ensign Sato exit Madame Chang's restaurant in San Francisco. Suddenly, two shadowy figures step out of an alleyway and order Phlox to accompany them. When the Denobulan voices his confusion, one of the men aims a disruptor at the doctor. Hoshi uses her knowledge of aikido against the men but another hooded assailant appears behind her and knocks her to the ground. The doctor is restrained and carried away as Hoshi lies on the ground, barely conscious. As her eyes flutter, the linguist hears one of the men say something in an alien language before disappearing...