An encounter refers to the the event when The Flagship makes contact with a battlegroup in either HyperSpace or TrueSpace, or with an inhabited planet (in TrueSpace). The encounter starts with a screen showing the image and the name of the planet (Deep Space if it occurs in HyperSpace and the planet is then randomly generated), as well as the size of the battlegroup. In the case of an encounters at homeworlds and other planets of interest, the battlegroup ships fill the entire screen, meaning that there is an infinite number of ships. At the end of a hostile encounter, the debris is scavenged, yielding RUs; however, if the Warp Escape Unit is used to flee the fight, debris is not collected.
At the beginning of each encounter, there is the option of either conversing with the aliens or attacking them. At this point, the game can also be saved, and certain game settings, such as music, sound, and the cyborg option, can be adjusted.