The ultimate weapon of the U.S.S. Discovery isn't its phasers or torpedos, but rather its unique propulsion system: the spore drive. Now the Discovery has accidentally slipped into the mirror universe where the previous I.S.S. Discovery has been destroyed. Several members of the I.S.S. Charon would like to capture the Discovery to use it for their own aims.

In Star Trek: Discovery – Black Alert, players divide into teams, and each team represents key members of either the U.S.S. Discovery or I.S.S. Charon crew. Players take turns activating locations on their ship, navigating through the network, and attempting to accomplish missions. One crew is trying to return home, while the other wants to capture their ship. Which team will emerge victorious?