Liam's got it right. From page 15 of the pdf:
"The focus of these scenarios is the ‘Mark’ – the unique character that the crew is trying to
take down. After everything else is set up, roll on the Mark Table to identify the target! The
Mark is then placed in or behind a randomly determined notable feature on the table."
How's your win/loss ratio on this play mode going? Mine's hovering around 60:40, with Pondo Pondo and Collen Preks handing me the most savage beatings to date, although the Complications may be responsible for a lot of that. Preks seems to love gangs of Networked Robots, and Pondo is absurdly lucky with Difficult Identification rolls, which have come up three times for them now.
My worst loss to date was to Tamix Phage but I refuse to give her much credit for it. Rolled Proximity Mines for a Complication and managed to lose both my officers to the things. Hit the first mate with a crit turn one, and then randomly pinged the captain twice in the next five turns.