Just as the crew is wondering why Destiny has dropped out of FTL, an alien ship is sighted in their path. Fears of another hostile alien encounter are quelled when an auto-piloted kino reveals the ship to be devoid of any life. Rush suggests that the ship be explored by an away team, and, of course, nominates himself to do the exploring. But Young won't let the scientist out of his sight, and so the volatile twosome is alone, again.
Because the last working shuttle crashed on the planet that took Riley's life, Rush and Young must don the space suits and use a kind of zipline to board the ship. They get the life support systems up and running, but then are jolted by a freak burst from the engines - it didn't last long, but the ship is now adrift, moving away from Destiny and snapping the zipline. If Rush wants to live, he's going to have to get Destiny to turn around and head towards him. The trouble is, he's not willing to let any of the crew know that he's unlocked the secret to full control of the ship.
Ginn and Eli have taken their relationship to the next level, and Simeon - the Lucian who was confined for violent behavior - doesn't like it. Just as he's trying to set her straight, however, Camille escorts Ginn to the communication stones for the dual purpose of having her deliver strategic information to homeworld command, and to allow Amanda Perry - the only person Rush trusts - to come on board.
Once she's acclimated, Rush uses the video interfaces of the two ships to send Amanda secret instructions on how to steer the ship. When Brody and the others discover Destiny changing course, they know something's amiss. Eli reviews the kino footage to glean information on Amanda's whereabouts, and the scientists head to what they soon learn to be the ship's bridge, with Amanda sitting in the captain's chair.
Young, meanwhile, has overheard Rush's exchange with Amanda, and thrashes Rush for withholding such valuable information. But soon their attention is grabbed by the fact that Destiny, helmed by an unpracticed pilot, has crashed into the alien ship, sending it spinning. Eli calculates the exact moment Rush and Young will have to launch themselves out of the ship in order to land safely on Destiny. Rush makes a clean landing, but Young jumps to soon. It seems he'll careen into space, but Rush makes a dash for him, grabs hold, and drags him to the safety of the ship.
With the life-threatening issues out of the way, the crew eagerly get to work on processing the fields of data unlocked with Destiny's master code. What's to be done about Rush's transgression will come later, it seems.
And Simeon, unaware that Ginn's body is occupied by Amanda's consciousness, seeks out a confrontation that reeks of malice.