SG-1 is providing security for three scientists who are conducting research on a far-off planet. Goa'uld warlord Khonsu arranges to capture the SG-1 team and O'Neill tells Jay Felger, nominally the group's leader, to use the gate and head back to SGC. Felger is quite enamored with SG-1, admiring their exploits and daring-do. Rather than follow O'Neill's orders, Felger and another scientist, Simon Coombs, transport themselves up to the Goa'uld ship. What the scientists don't know is that SG-1's capture is a ruse to allow Khonsu, who is actually a Tok'ra, to pass on information. O'Neill is quite annoyed with the two scientists but their presence proves useful in the end.

Riding in the elevator in the SGC, O'Neill is visited by Daniel Jackson who needs his help. Daniel tells him that Anubis is headed for Abydos to search for something called the Eye of Ra, a relic that would make Anubis all-powerful. It's essential that SG-1 go to Abydos and secure the Eye but no has seen it - including Daniel - nor has anyone ever been able to find it. On the planet they see their old friend Skaara and with Daniel's help locate the Eye. They also find a tablet that speaks of a lost city of the ancients. When Anubis and his troops land in force there is little anyone can do to stop them. In the end it's left to Daniel to decide if he will try to stop Anubis - thereby breaking a cardinal rule of the Ancients.

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.

Anubis's super weapon has been put out of commission, but Yu's fleet has been diverted to the other side of the galaxy by Yu himself, allowing Anubis to escape into hyperspace. Jonas has been captured by Anubis and Daniel is still aboard Anubis's ship, evading capture. Anubis uses the mind probe on Jonas, learns of Naquadria, and begins his attack on Kelowna. The Kelownans seek aid from the SGC. Jack and Sam arrive on Langara to discover that the Kelownans have given Anubis Naquadria in order to secure their safety. They communicate with Daniel who is attempting to free Jonas. Teal'c has convinced Yu's first prime to seek a new leader of the System Lords, Ba'al.

With Jack having the knowledge of the Ancient repository once again in his mind, he and Daniel attempt to unearth the location of the Lost City of the Ancients. Bra'tac, bringing with him the news of an impending attack on the Tau'ri by Anubis, takes Teal'c to help him acquire ships and warriors for the defense of Earth. Dr. Weir attempts to cope with the overwhelming nature of her new job, while also dealing with the unrelenting ego of Vice President Kinsey.

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.