While redialing old Stargate addresses, the SGC discovers that a gate that was previously buried has become uncovered. They send a probe through and find two archaeologists. However, when they travel through the Stargate, they find that it is located in a society in civil war: one continent believes that the people were created by a Goa'uld, whilst their enemy believes that humans arrived from another planet - by the Stargate. O'Neill, Carter and Jackson are captured by the authorities and questioned, but Teal'c is wounded and blinded. Can he help SG-1 escape the hostiles and get back through the Stargate?

As Jackson suffers from a fatal dose of radiation, he struggles with the value of his life while his friends deal with the emotional and diplomatic repercussions.

SG-1 brings back an Ancient device, the purpose of which is unknown. When Jonas touched it the device activated. Upon reaching the SGC Jonas sees a large red insect fly into a wall, but no one else can confirm his sighting. The SGC is put into lockdown, but nothing is found. Jonas suspects that the Ancient device is causing his hallucinations, but to his dismay it is set to be shipped to Area 51. When Teal'c and Jack see the bugs as well, General Hammond decides to let Jonas take a crack at deciphering the Ancient text on the device.

The documentarian still a thorn in their side, SGC encounters an unforeseen predicament. With half of SG-13 off-world engaging enemy Jaffa, SG teams 1, 5, and 7 go in as backup. In the midst of heavy fire, O'Neill takes a staff blast to the chest. Many deaths from the encounter hit SGC hard and Senator Kinsey orders a full investigation into the matter.

As the new head of the SGC, General O'Neill is beginning to feel the weight of his load, and he starts to have second thoughts about the whole idea, questioning his own competency.

Sam and Jacob are on the planet Dakara trying to configure the Ancient's device to destroy the Replicators once and for all, helped partly by Ba'al and Daniel, who succeeds in freezing the Replicators by manipulating Carter's duplicate.

SG-1 returns early from a mission only to realize that they and Gen. Landry aren't on the same page as far as the the mission they've just completed is concerned. The confusion is quickly resolved when the "real" SG-1 returns at the correct time. Dr. Lam examines them all and concludes that they are identical and thinks they might be clones. Sam however thinks they may have come from a parallel universe as the result of the black hole they created when they destroyed the Ori beachhead. As more SG-1 teams arrive from other alternate universes, one of them includes Dr. Fraiser and another includes the Tok'ra Martouf. It's left to Sam and Martouf to find a way to send them all home.

Vala is kidnapped by agents of the Trust who are trying to find an ancient treasure when an accident causes Vala to forget who she is.

Cameron Mitchell must go undercover inside the Lucian Alliance to find the location of the hijacked Odyssey.

During a failed experiment, Samantha is transported into a parallel universe where she cloaks Earth to save it from an Ori attack. Getting back to her own universe is not met with sympathy.

General Landry accompanies SG-1 on a mission to collect the knowledge of the Asgard. When the Ori show up, however, Sam is forced to evacuate the crew. Landry and SG-1 stay aboard, but are stuck helpless in a time dilation field for decades.