The US and Russia reveal Stargate Command and its operations to representatives of the other permanent members of the United Nations Security Council.

A group of nomads on an alien planet find Daniel Jackson naked in the middle of ruins and take him in. Jonas translates the tablet Daniel said was important and discovers that it describes the last city the Ancients were building before the plague. He surmises that the list of addresses Jack put into the computer while storing the Ancient data were Ancient outposts in temporal order. Thus the last of the addresses should be the "City of the Lost". SG-1 visits the planet and happens upon the nomadic people, now inhabiting the ruins of the Ancient city. There they find Daniel, but discover his memory is gone. They must recover his memories in order to discover the secret to defeating Anubis.

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.

The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.

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.

Sam manages to activate an Ancient device they found at the Glastonbury site and she and Mitchell are shifted into a phase that makes them invisible to everyone. Daniel soon figures out just what is going on but Dr. Lee's proposed solution sends Daniel to the same plane as Sam and Mitchell. There he is able to translate information explaining that Merlin had created a weapon against the Ori - and provides a gate address where it can be found. Meanwhile, Teal'c travels to a Jaffa planet that has sent out a distress call. The two events are related.

The team goes off-world and ends up in serious trouble. Meanwhile, Landry is faced with having to decide whether or not Vala can be trusted to remain at the SGC.

SG-1 is caught in the middle of a war after the Jaffa use a powerful weapon to kill 10,000 Ori followers.