The game begins with the USS Enterprise (NCC-1701-D) in orbit around a red giant star near the edge of the Neutral Zone (the star adversely affects Romulan sensors, rendering the Enterprise undetectable). They are monitoring the border in response to increased Romulan activity; the Romulans recently lost contact with a vessel patrolling the Neutral Zone. Starfleet had agreed to assist in any investigation attempt as a sign of goodwill. The Romulans refuse the aid, and prefer to handle things on their own, which naturally prompts Starfleet to increase border patrols.
Immediately upon beginning play, the Enterprise receives a distress signal, broadcasting on all frequencies. It was sent out by one Dr. T'Laris, a Vulcan geologist stationed on a planet in the Codis Mu system (Codis Mu VI), and in the message she notes that her dig site was recently attacked by Romulans, and that the assailants are still present. The Enterprise responds to her plea for help and sets a course to her dig site.
As the game progresses, the player learns more about the missing Romulan vessel's mission, and of the IFD. The Enterprise also makes contact with an alien race known as the Chodak, hostile mollusk-like creatures who constantly accost the Enterprise as it traverses known space gathering clues about the IFD. There are also mentions of a now-extinct race called the Senatorious who were the last race to possess the IFD; the reason it resurfaced is because the Senatorious understood that they'd been using the IFD for their own benefit at the cost of all other races, and judiciously decided to send it ten thousand years into the future, in the hopes that civilizations then could put the IFD to use for the mutual benefit of all races. There is one more race, the gaunt Eunacians, which are encountered only once and, after the Enterprise repairs their ship, tell Jean-Luc Picard of the IFD Trials and the Eunacians' intention to participate. However, with their ship crippled, and the rest of their race residing in the Gamma Quadrant, they entrust the Federation with recovery of the IFD, and its judicious use.