 The original concept of an episode involving alternate realities was a room in Atlantis that shifts into alternate realities . However , the idea had several issues , including the possibility of no Atlantis in one reality , so Robert C. Cooper suggested using the Daedalus . The final draft of " The Daedalus Variations " was completed on February 11 . On February 12 , the prosthetics meeting for the episode , as well as " The Seed " , " Broken Ties " and " Whispers " took place , which most likely involved the unknown aliens featured from the episode . The appearance of the aliens was revealed in the advertisement for the episode on July 27 . In an interview with episode writer , Alan McCullough , he described the episode as a " great team show " , and a " visual effects spectacular . " On March 10 , Captain Sobol was cast . Sobol was the alternate commander of the Daedalus , rather than Colonel Caldwell ( Mitch Pileggi ) . By the time the episode aired , Sobol was female ( portrayed by Tracy Waterhouse ) , she held the rank of Colonel instead , and her name was spelled " Sobel " . 
