Universe II is the sequel to Omnitrend's highly complex space simulation Universe. It takes place 20 years after the original game. A second hyperspace booster has been found, so there is hope that communication with Earth will be re-established in the foreseeable future. Still, the situation in the Local Group is tense. Two rival governments have formed: The Federated Worlds and the United Democratic Planets. Currently, travel and trade between the two is ongoing, but everyone fears the tensions will lead to all-out war.

The player takes the role of an undercover operative for the Federated Worlds. Disguised as a free trader from Vromus Prime, they will have to earn a living for themselves, because the FW only gives out money or equipment for special missions.

As in the original game, there are many ways of spending one's time and earning credits in the Local Cluster. Trade, exploration, passenger or freight transport, mining, smuggling, bounty hunting or piracy are among the many options.