With time running out as the ship’s systems malfunction, Young’s people must work with Kiva and her men to save the ship before they all die.

Commander Kiva of the Lucian Alliance has managed to board the Destiny and has taken several of the crew hostage.

Rush returns to Earth to find a way to prove Telford is a spy.

Dr. Tamara Johansen tries to track down what is causing the crew to hallucinate.

The crew calls upon a brilliant scientist from Earth to help find a solution when a drive module on the Destiny explodes due to an overload.

The crew calls upon a brilliant mind from Earth to help in a crisis — a quadriplegic scientist who temporarily takes over Wray’s body.

Dr. Rush links himself directly to the destiny’s computer hoping it will reveal the code needed to control the flight path.

Destiny stops near a planet with an abundance of food and water but its countdown clock isn’t running.

Dr. Nicholas Rush and Chloe suffer nightmares following their ordeal on the alien vessel, and Rush suspects that a tracking device may have been placed on the ship’s hull. Later, a splinter group on Destiny executes a coup with life-threatening consequences.

Using a piece of Ancients technology, Colonel Young accidentally ends up on an alien vessel, and then, suddenly, finds himself back on the Destiny. Meanwhile Rush is captured by some aliens and they put him into the tank.

Lt. Scott and Camille return to Earth via the communication stones to spend time with those they left behind. On the Destiny, the crew explores new sections of the ship, which yields the discovery of a promising Ancient device.

An away team finds a kino beside a Stargate on a jungle world, which contains video footage of the team that was shot prior to their arrival. Then, an illness cripples the team, forcing them to quarantine themselves on the planet.

General O’Neill (Richard Dean Anderson) wants Col. Young to implement a high-risk plan hatched by IOA scientists that could possibly return the Destiny crew to Earth. Elsewhere, Eli and Chloe use the communication stones to visit their loved ones, culminating in a trip to a club. Carlo Rota, Janelle Monáe.

The ship’s water supply dwindles, prompting Col. Young and Lt. Scott to visit a frozen planet in search of drinkable samples. Meanwhile, the crew attempts to snare an intruder

The crew are in close proximity to one of the three planets. Col. Young tells everyone that only seventeen people can go in the shuttle and a lottery will determine their fate.

Lt. Scott and Dr. Rush travel to a desert planet to locate a mineral essential to Destiny’s life support system.

The evacuees from Icarus Base discover that the life-support system on the Destiny will fail in a matter of hours.

When a research team is forced to evacuate their secret base, they find themselves on board an Ancient vessel that is millions of years old — with failing life support and no way to gate home.