Now firmly in control again, Col. Young and the other military personnel try to find a way to live with the civilians who tried to take control of the ship. When the Destiny prematurely drops out of FTL due to a computer glitch, they find both a sun and an Earth-like planet that should not be there. Rush concludes that the entire system was created by an alien race that is far beyond their imaginations. With the ship malfunctioning and a month's worth of repairs before it can jump again, several of the military and civilians decide to spend time on the planet. Hard feelings from the mutiny persist and it's an opportunity for everyone to mend fences. When the time comes to return to the Destiny, several of them decide they want to stay on the planet. Young is prepared to let them stay, but he imposes severe conditions.

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

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

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

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.

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.