Did Kirk, Spock, and McCoy have an epilogue on the bridge at the end of each episode (like in the original show) or was this only in a few of the episodes? (It's been so long since I've played it ... awesome game though.)

Each episode finished up on the bridge, similiar to the actual series, where closure for the episode was provided. An effort was made to ensure that all the regular Star Trek bridge crew (Uhura, Scotty, Sulu, and Chekov) took part in the conversation, so it was not limited to Kirk, McCoy, and Spock.