The Lucian Alliance is still in control of the Destiny and Col. Young is determined to get it back under his control. Young and most of his personnel are prisoners, however, leaving it to Rush, Lt. Scott, Sgt. Greer, Eli and Chloe to find a way to get control of the ship. They are left alone on the Destiny when Young and the prisoners are dispatched to a nearby planet. When they take possession of the control room, Rush devises a plan that will likely result in the death of the Lucian Alliance members but also any of their colleagues that might still be on board. Meanwhile, TJ is unconscious recovering from her wounds but seemingly awakes in a perfect dream where she and her newborn are joined by crew members from the past.

Rush finally gets full control of the Destiny but it's not long before mistakes are made.

The crew comes across a ship that is virtually identical to Destiny. The two ships automatically dock with each other and begin transferring data between systems. No one appears to be aboard the new ship, but Scott and Greer discover a hold with a series of gates, presumably being transported to various sites. The scientific team thinks that combining the power of the two ships may allow them to open a gate to Earth. It all goes wrong, however, when the new ship begins to drain Destiny's power. Nor, it turns out, are they alone on board the new craft. Meanwhile, Col. Young continues to clash with the remaining members of the Lucian Alliance, who want to be freed from custody. Several of the civilians think he should give them a break, but he's convinced they're a threat. TJ is still dealing with her emotions over the loss of her baby.

Eli rushes back to Earth using the communication stones when he receives word that his mother is hospitalized and in declining health. She's stopped taking her medication and is clearly depressed over the fact that Eli has never been in touch with her. Eli has to decide whether or not to tell her the truth. Camile Wray also visits Earth to spend time with her partner, Sharon Walker, but something is clearly wrong. Chloe has been out of sorts lately and begins sleepwalking. A concerned Lt. Scott finds something startling in her diary. Col. Young decides to release the Alliance members from the brig but one of them is having difficulty fitting in.

While on a planetary expedition, Lt. Scott is infected by a plant and he now has a fungus-like growth on his left arm. TJ has tried everything known to her but she cannot get the fungus to stop spreading. Col. Young refuses them permission to return to Destiny to prevent the spread of the unknown disease and they face the prospect of having to surgically remove Scott's arm. In his unconscious state, Scott imagines himself returning home to Cloverdale where he is to be married to Chloe. In his dream-like state, roles and identities have changed: Sgt. Greer is his best friend and is with him to act as his best man; Eli is Chloe's brother; Col. Young his father; TJ is a paramedic who treats him after he loses consciousness; and Dr. Rush is the Minister who will marry them.

After returning from Earth (via the communication stones), Col. Young is somewhat depressed as his wife asked him for a divorce. He's drinking heavily and begins to have a recurring dream where Destiny is attacked by the aliens they had earlier encountered. They are demanding Chloe's return and in the first few dreams, his refusal to do so leads to Destiny's destruction. In a later dream, he eventually relents and hands Chloe over to them, leading to a major confrontation with Lt. Scott. He is convinced that his dreams are a premonition but Dr. Rush has a different interpretation. As well, Rush still hasn't told anyone that he now has complete control of the ship. Meanwhile, Eli may have found his soul mate when one of the Lucian Alliance members shows an interest in his work.

Destiny comes out of hyperspace and the crew finds itself facing an abandoned space craft. Col. Young and Dr. Rush go aboard and manage to start basic systems but a sudden engine start propels them too far from Destiny to be able to return. Rush confides in a colleague who is on board using the communication stones, Amanda Perry, about the control room and his ability to control all of Destiny's systems. Word soon spreads leading to yet another confrontation between Young and Rush. Ginn and Eli seem to be getting along well but she is asked to travel to Earth to provide information on a possible Lucian Alliance attack. Simeon is concerned that Ginn is giving away their secrets and is clearly intent on doing something about it.

Simeon has killed a team member - whose body contained Dr. Amanda Perry's consciousness - and taken Lisa Park prisoner before using the gate to get to a nearby planet. An outraged Dr. Rush sets off on his own to find him but Lt. Scott and Sgt. Greer soon join him. Simeon is quite happy to lead them on a chase and taunts Rush at every opportunity. When Rush finally catches up with him, he has a surprise for him. He may have acted too quickly however. On board the Destiny, Eli is doing his best to slow the jump clock to give those on the planet more time. Chloe is the one who comes up with a solution to their problem.

Destiny comes out of hyperspace only to find one of their own shuttles asking for permission to dock. Aboard are Dr. Caine and the others who had opted to re-settle on a planet they had discovered. They claim to not know what is going on and the last they remember is that they were still on the planet when they went to bed the previous evening. TJ hopes that her baby will be with them but Caine has no memory of her visiting them. Most of the returnees seem to have few memories of their time on the planet and Camile Wray thinks that the aliens may have wiped their memories clean. She suggests hypnosis as a means of unlocking their minds. Eli meanwhile is worried about Chloe, as is Lt. Scott, but her transformation into an alien being is continuing.

After identifying an energy pattern that may signify the existence of intelligent life, Destiny is rerouted to the site only to find the results of what must have been an epic battle. Debris is strewn everywhere and Col. Young dispatches Lt. Scott, Sgt. Greer and Adam Brody in the shuttle to investigate one of the ships - the type that he and Dr. Rush had only recently explored. The team has little time to find anything before they realize that not everything in the battlefield is debris and attack drones are lying in wait. Destiny's engines are off-line however and their shields are weakening under an endless assault when someone from their past comes to the rescue. It's not going to prove to be smooth sailing however. Meanwhile, Chloe's transformation is advancing rapidly. She manages to escape custody and heads straight for the bridge.

Destiny comes out of hyperspace and come under attack from the command ship. Chloe has escaped from the brig and sent a signal for help. Eli suggests jamming their communications signal, which seems to work. The ship is damaged however and it will take several hours to repair the shield generator and a second cluster of attack ships are en route to them. When the shuttle is trapped as it tries to recover one of the attack drones, Col. Young decides to offer Chloe in return for freeing it. When the second wave of drones arrives, they find a way to add to their firepower.

Destiny is in poor shape following its recent battles and has virtually no back up systems remaining. As the ship approaches a star for refueling, Eli wants to test his theory that he can dial Earth. While the simulations suggest that it will work fine, Rush is dead set against, arguing there are too many anomalies in a star for it to work. Most are suspicious of his motivation however. With most of the crew in the gate room waiting to leave through the gate they receive a message - from a second Dr. Rush coming toward them in the shuttle. He claims to have traveled back in time 12 hours and relates what happened. The anomaly and time shift also present a solution to their need for redundant systems.

When Camile and Sgt. Greer use the communications stones to return to Earth, they arrive to learn there is a high state of alert in anticipation of an attack from the Lucian Alliance. They've barely arrived when an explosion traps them in the building where they find high levels of radiation - and where, they are told, there is a large bomb still waiting to go off. On board Destiny meanwhile, visiting Senator Michaels and Dr. Andrew Covel arrive to assess the viability of the mission and determine whether the government should invest in a new Icarus base.

Six days have passed since Destiny lost contact with Earth and they have no idea whether Washington D.C. was destroyed. They're running tests around the clock to try to re-establish communications using the stones. When Chloe's turn comes up, a new consciousness appears in her body - that of Ginn, who everyone thought had died along with Amanda Perry when she was killed by a member of the Lucian Alliance. No one is quite sure what or how it's happened but it soon becomes apparent that Ginn's consciousness will have to somehow be harnessed or there will be a major risk to Chloe. Eli is thrilled at being able to spend some time with Ginn but is worried that he will again lose her. TJ meanwhile determines that Volker is suffering from advanced kidney disease and needs a transplant immediately. A suitable donor is found but TJ isn't sure she can perform the operation.

Aboard Destiny, Rush has strapped himself into the chair and entered a virtual reality world where he can spend time alone with Amanda Perry. They very much enjoy their time together but when it comes time to return, she tells him that Ginn is blocking his return. They undertake a number of maneuvers and he seems to return but he soon realizes that Amanda has created a program from which there is no escape. Ginn manages to appear before Eli and he realizes what he has to do to ensure Rush's safe return. On Earth meanwhile, Homeworld Command is trying to negotiate a deal with the Langarans which will allow them to use their power source for gate travel. Langaran Ambassador Ovirda refuses, leading to concerns that they may have already made a deal with the Lucian Alliance. With Dr. Rodney McKay and Richard Woolsey, they devise another plan.

With the ship out of hyper space, a team goes to a nearby planet and are pleased to find that game may be available. They soon find themselves the hunted and the object of a predator of some sort of highly intelligent animal. The group is attacked and TJ and another are taken to the creature's lair, apparently being kept for a later meal. Greer and the remaining members of the Lucian Alliance try to locate them. Meanwhile, aboard Destiny, a section of the ship containing stasis pods is found by Rush, Eli and Brody. Rush seems unmoved by the find and tells Eli and Brody to just continue with their usual work routine. They're unable to do so and begin to explore the pods when suddenly Brody finds himself trapped in one and frozen. While Eli desperately tries to get him out there, Rush is on the bridge manipulating the situation.

Destiny once again comes under attack from the drones they previously encountered leading them to wonder just how the drones and their control ship manage to find them so soon after virtually every jump. More intriguing to everyone however are the people they find on a planet who claim to be the descendants of Destiny's crew who founded their civilization nearly 2000 years ago. They are only a small party from their home world but have been unable to return there. Eli surmises that the alternate Destiny that they believed was destroyed by falling into the sun may in fact have been thrown even further back in time, leading them to be the founders of the new civilization. After the drones again find them and the descendants camp is destroyed, they are all taken aboard Destiny for the return trip to their home world but are disappointed with what they find when they arrive.

The shuttle lands on Novus and the recon team explores a bunker where they find an extensive library and archive that cataloged virtually all of the activities of the original colonists. The kinos and other recordings reveal the key events in their alternate lives - people die, they marry and they have children. For some however, knowing what happened to their alternate selves raises doubts in their minds as to their own future. The planet is clearly not stable and earthquakes are getting more severe forcing an immediate departure. They do learn that the population managed to evacuate Novus successfully.

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 have only one more try before running completely out of fuel. Eli suggests they go through a Blue Super Giant 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 Park also stays behind to collect some of the medicinal herbs they've grown only to be trapped just as Destiny goes through the star. On the planet, Young and the others find evidence of a destroyed civilization - and the drones which destroyed it.

Eli and Rush have found a way to identify the location of drone mother ships using 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.