Scott and Greer are seemingly killed while on the hull of Destiny; Rush tries to undermine the ship's shields to force the Lucian forcess to surrender; Chloe makes an amazing recovery; T.J. finds herself on an alien planet with her baby; and the Lucian forces disagree on how to maintain their hold on the ship.
Songs: Mumford and Sons -- After The Storm
Rush secretly gains access to the ship's hidden bridge and brings Destiny out of hyperspace so they can get food at a nearby planet. However, Rush miscalculates and the shuttle crashes. Meanwhile, Young and Camille disagree over how to deal with the Lucian prisoners.
The crew encounters another seed ship, and Destiny auto-docks with it. They realize that it may hold the key to them getting home... but it also holds a deadly danger.
-- Sort of Revolution
While Eli and Camille travel to Earth to deal with personal issues, the Destiny crew realizes that Chloe has become possessed by an alien intelligence... and it wants to learn everything about the ship.
Scott is infected by a highly contagious plant organism, and can't be brought back to Destiny for fear of infection. As the crew on the planet try to improvise a cure, more of the plant organisms close in... and Scott hallucinates that he's in the town of Cloverdale on the day before his wedding.
Young is plagued by mysterious dreams where Destiny is destroyed by alien attackers no matter what he does.
Destiny encounters an alien derelict, and Rush and Young board. But when they're stranded, Young confronts Rush about what he's hiding.
Simeon kills Dr. Amanda Perry when she is using Ginn's body, and he escapes from Destiny via the Stargate to a nearby planet. Rush goes after him, intending to kill the man who murdered his lover. Meanwhile, a distraught Eli tries to stop the countdown clock so that Destiny can remain within range.
The others who chose to remain on the alien construct planet appear in the shuttle, floating in space next to Destiny. Young must decide what to do with them, and determine if they are who they claim. Meanwhile, Chloe tries to make her peace with Scott and the others as the alien pathogen continues to transform her.
The crew uses their control of Destiny to investigate radiation signals, and discover a graveyard of ships, leftover from some great battle...and not all of the ships are dead. Meanwhile, an old friend returns at the ship's time of greatest need, and Chloe continues to fall under the sway of the alien pathogen.
Destiny survives the battle against the drones thanks to Chloe summoning the aliens that have been pursuing them, but the crew realizes that they are out of options... and turning Chloe over to her former captors is their only choice.
In the wake of the Cluster attack, the crew must consider abandoning Destiny, and Eli comes up with a way to dial the ninth chevron. However, as they begin evacuation proceedings, a Rush from 12 hours in the future arrives to warn them that they're pursuing a fatal plan of action.
Camille and Sgt. Greer switch bodies with a visiting senator and scientist, but are trapped when Homeworld Command comes under attack by the Lucian Alliance. Meanwhile, the senator assesses the viability of Destiny.
While waiting to regain contact with Earth via the communication stones, Chloe's body is taken over by a foreign consciousness. While the crew tries to deal with the repercussions of this new presence, Johansen finds herself faced with a medical dilemma.
Songs: Richard Strauss -- Also Sprach Zarathustra
Richard Woolsey of Homeworld Command tries to convince the government of the planet Langara to dial Destiny and establish a supply line, but Telford and Young suspect that they have already made an alliance with the Lucian Alliance. Meanwhile, Rush and Amanda try to find a way to be together physically.
A team from Destiny is attacked while exploring an alien planet, and two crew members are abducted by a native creature. While Greer is forced to team up with Varro to recover them, on Destiny Eli and Brody examine newly-discovered stasis pods and get in over their heads.
To evade a wave of attacking drones, Destiny enters FTL and comes upon a planet settled by the descendants of the Destiny crew from the alternate timeline.
The Destiny crew take the Teneran settlers, the descendants of their counterparts from the alternate timeline, back to their homeworld of Novus, only to discover that the civilization has abandoned the planet due to extreme volcanic activity.
When the command ships blockade stars along Destiny's path, the crew must find a different, superhot star to recharge at. Eli and Rush are forced to pilot the ship in, while the rest of the crew evacuates to a nearby planet... only to discover that the drones are already there.
The crew of Destiny must make a final and potentially fatal decision to evade the command ships and continue along their designated course to find ultimate answers.