The second season of Stargate Universe was announced by Syfy on December 13, 2009. The second season consisted of 20 episodes, which began airing on September 28, 2010, with the episode "Intervention". The first five episodes were reserved by the primary series writers. New to join the writing team were Remi Aubuchon (Caprica, 24) and Linda McGibney (Homicide: Life on the Street, Chicago Hope); Aubuchon had responsibilities for writing episode 9, while McGibney outlined an episode in the second half with Brad Wright. Filming started on March 10, 2010 with fourth episode "Pathogen", directed by Robert Carlyle (his directorial debut) Filming was delayed somewhat due to the 2010 Winter Olympics, which took place in Vancouver.
Season two of Stargate Universe expanded upon the show’s mythology, giving viewers new insights as to why the Ancients launched Destiny millions of years ago. Among such insights was the fact that Destiny actually has a destination so important that it overshadows the desire for the crew to get home, and that by pursuing onwards toward this destination, it may in fact allow them to get home. Another feature of season two was a gigantic battle in space featuring an armada of alien spaceships. Furthermore, season two saw appearances from actors that previously appeared in Stargate SG-1 and Stargate: Atlantis, including David Hewlett and Robert Picardo. The Stargate: Atlantis character crossover occurred in episode 15, titled "Seizure", but did not shed light on the fate of Atlantis following the finale episode "Enemy at the Gate.
Dr.Nicholas Rush discovers the bridge, but keeps it secret from the rest of the expedition. Suffering from a food shortage, the expedition sends an Ancient shuttle to a planet near which Destiny stops. A shuttle malfunction forces the team sent to the planet to try to find a way to reactivate the disabled Stargate before they get permanently left behind.
Dr.Nicholas Rush and ColonelEverett Young investigate an abandoned alien craft which is just outside the Destiny. When the craft begins to drift away from Destiny, stranding them aboard, Rush must find a way to get Destiny to catch up to them without revealing his secret.
The members of the crew left behind on the artificial planet are suddenly returned to the ship with their memories mostly wiped. Soon one of them drops dead for no apparent reason, and they have to find out what happened on the planet before it's too late.
Eli Wallace's plan to dial Earth using power of the star is about to be executed, but interrupted with discovery of the shuttle piloted by Dr.Nicholas Rush, who traveled back in time after the plan got executed but had gone wrong.
Returning the settlers to their home planet Novus, the Destiny crew discover the planet has been abandoned and on the verge of seismic destruction. They raid abandoned fallout shelter for supplies and find records of founding of Novus civilization.