When the dradis picks up an unknown ship of enormous size closing in on the fleet, the Galactica goes to full alert, launching fighters and sending the CAP, which is led by Apollo, to intercept. A vessel this size could only be a Cylon basestar, yet a stunned Mr. Gaeta announces that he’s picking up a Colonial transponder from the approaching vessel. Tigh thinks the Cylons are now using Colonial transponders as a way to lure them into a trap. But Adama isn’t so sure; he orders a hold on both weapons and a jump for the overall fleet, and opens communications between the ships. His hunch turns out to be correct: the Colonial transponder is legitimate, as it belongs to the Battlestar Pegasus, under the command of Admiral Cain. Once the Pegasus joins the fleet proper, Cain meets with Adama and Roslin in Adama’s quarters aboard Galactica.

At the same time, in another section of Galactica, Tigh shares a drink with Fisk, his XO counterpart from the Pegasus. While Cain relates the story about how the Pegasus managed to survive the Cylon assault on the shipyard where it had been docked for an overhaul (Cain ordered a blind jump, which was a daring and risky move) Fisk tells Tigh some pretty scary stories of his own. Fisk rose to the rank of XO after Cain shot his predecessor dead when the man refused to carry out a suicidal order she gave. Deck Chief Tyrol inadvertently discovers another dark side to the Admiral when he encounters the Pegasus’ Deck Chief, who is actually a civilian who was "recruited" into the service when Cain and her crew came across the civilian ship he was aboard. And despite her initial promise to leave Adama’s command alone, Cain promptly shakes things up by integrating the Battlestar crews, starting with Apollo and Starbuck, who she orders to report to Pegasus. While Adama reluctantly follows orders like the good Colonial officer he is, the breaking point for him comes when a vile incident occurs between the imprisoned Sharon and a Pegasus officer named Thorne.

Pegasus is a remake of the original series two-part episode which starred Lloyd Bridges as Commander Cain, a swaggering John Wayne-like warrior who still wore a Viper pilot’s uniform and whose only orders were to attack. For the remake, Cain was given a sex change and increased in rank to Admiral, which offered more grist for drama, since the Galactica crew--including Adama--have no choice but to follow her orders. Michelle Forbes (Homicide: Life On The Streets; Star Trek: The Next Generation) very capably handles the role of the hard-driving Cain. Michael Rhymer, who directed the original mini-series, as well as "33", the first episode, returns to handle the directing chores on Pegasus, and he effectively builds up the tension between the two battlestar commanders and their ships right up to the shocking ending.