Attacking drones return when the Destiny tries to recharge in a star. Eli proposes a risky alternative, which requires the rest of the crew to gate to a nearby planet for safety, where they find an abandoned city.
Destiny reaches an abandoned modern civilization on a planet in the throes of seismic destruction. While the crew retrieves valuable data archives stored underground, Rush discovers a possible way to help the planet's survivors.
Rush slips into a coma in the neural interface chair, and Amanda connects with him in the ship's matrix, but Ginn informs Eli of a problem with that scenario. Elsewhere, Dr. Rodney McKay's plan to dial the ninth chevron address hits a snag.
Eli may have found a way home, but Rush believes the plan could go catastrophically wrong. After experts on Earth decide in favor of Eli's plan, Rush announces his intention to remain on the ship and calls for volunteers to stay with him.
The Destiny follows a remote energy signature to an area of space strewn with destroyed ships that are initially believed to be the remnants of an ancient battle. Elsewhere, Eli grapples with how he's going to tell his mother what really happened to him.
Simeon makes a violent escape from the Destiny. Homeworld Command believes that Simeon has information that could prevent an attack on Earth, spurring a manhunt on an alien world to capture Simeon alive.
Rush devises a risky plan to use radiation from the binary pulsar to force the Lucian Alliance to cede control of Destiny. Meanwhile, a critically injured lieutenant Johansen dreams of a rustic life with her baby in the Season 2 opener.