Black Box missions only appear as a secondary objective.
Black Box missions are very similar to the Uplink and Refueling stages of a Salvage Operation. The equipment must be repaired, after which the team has to stay inside a visible radius, fighting off creatures until the progress bar completes. The progress bar will move faster the more players remain within the radius, and will rapidly decrease if no players are within the radius. Mission Control will chastise the players until they return to the zone. If the progress bar is completely depleted, you will be able to retry the Black Box. Players who are downed within the triangulation zone are counted as outside the zone, and will not advance the progress bar.