The USS Discovery's ultimate weapon is not its phasers or torpedoes, but its unique propulsion system: the spore drive. Now Discovery has accidentally ended up in the mirror universe, where the previous ISS Discovery has been destroyed. Several members of the ISS Charon want to capture Discovery to use it for their own purposes.

In Star Trek: Discovery - Black Alert, players divide into teams, with each team representing key members of both the USS Discovery and the ISS Charon crew. Players take turns deploying locations on their ship, navigating the network and attempting to complete missions. One crew tries to return home, while the other team wants to capture their ship. Which team will emerge victorious?