Eli and Rush have found a way to identify the location of drone mother ships using the Destiny's long range sensors. The bad news is that the Drones seems to be awaiting them at every possible stop along Destiny's path. They find a temporary solution to neutralize the mother ships but realize that they cannot engage in a major battle every time they need to re-supply. Eli suggest that they use the stasis pods for the crew and jump to the next galaxy, a trip that will take three years. All goes well until they realize that one of the pods has been damaged and one person will have to stay behind in the hopes of fixing the unit in the short time available or die.

While attempting to return a group of colonists to their home, the crew finds that the planet is on the verge of seismic destruction.

Rush travels back in time to avert a disaster, meeting a past version of himself.

The Destiny needs to be refueled but every time they come out of FTL the drones seem to be waiting for them. It's not obvious how the drones know they're there but it doesn't matter a great deal since they only have one more try before running out of fuel completely. Eli suggests they go through a blue supergiant star, though the heat it creates might destroy the ship. They have little choice so Col. Young evacuates everyone to the only planet available with the exception of Eli and Rush. Lisa also stays behind to collect some of the medicinal herbs they've grown only to be trapped just as the Destiny goes through the star. On the planet, Young and the others find evidence of a destroyed civilization - and the drones.

Destiny comes upon a colony where the people claim their civilization was founded two thousand years earlier ... by Destiny's crew.

Rush and Young investigate an abandoned alien craft which is just outside the Destiny. While they do this, the crew onboard the ship find the bridge and discover that Rush is responsible for the countdown clock not activating when the ship emerges from FTL.

The crew encounters a ship remarkably similar to Destiny, which may hold the key to their returning home.

Simeon makes his escape from Destiny, sending Nicholas Rush on a vengeful mission. But Young and Greer attempt to retrieve Simeon unharmed.

The crew's new-found control over Destiny's flight path introduces new risks when they find themselves in the middle of a war between two races.

Chloe's body is taken over by another consciousness. Meanwhile, Dr. Volker is stricken with a mysterious illness.

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.

Locked in a battle with a Drone Command Ship, the Destiny is surprised by the arrival of the Aliens that abducted Rush and Chloe.

Camille and Sgt. Greer are trapped when Homeworld Command comes under attack.

Everett and the crew continue their efforts to save Destiny while holding off the Lucian Alliance invaders.

Desperate for food and water, Rush directs the ship to a planet that has been locked out of Destiny's controls. Young and Wray clash over what to do with the Alliance prisoners.

Young is plagued by mysterious dreams where Destiny is destroyed by alien attackers no matter what he does.

Chloe behaves in a bizarre way, prompting a search of her quarters, where Lt. Scott finds a journal penned in an alien language. Elsewhere, Eli copes with his mother's medical condition.

An alien creature attacks an exploration team from Destiny, taking two crew members captive.

Members of the crew left behind in another galaxy make a shocking return to Destiny.

When Scott's team explores a new planet, a plant-like organism infects the lieutenant, causing him to hallucinate a life back on Earth where he is getting married.