Following on a Tok'ra tip, SG-1 goes to a planet where they find the hated Apophis, nearly dying and under attack by death-gliders. They get back with him, realizing he was tortured by a rival system-lord with lasting harm. Apophis demands sanctuary, provided Dr. Fraiser can save his life, at least on account of the human host, but without a sarcophagus the prognosis for his symbiont is lousy; he offers all his Goa'uld knowledge in exchange for a new host, i.e. his life, revealing he was defeated by the terrible Sokar, once supreme system lord till an alliance lead by Ra and Apophis unseated him. The confrontation with Daniel, on account of Amaunet/Sha're and their son Klorel, and with former prime Teal'c, is bitter for all three. The Tok'ra send Martouf to warn the Tau'ri must hand over Apophis, but their warning is ignored- until Sokar proves he can bombard the iris with accelerated particles and ultimately cut through it, so the White House orders his extradition, but before they can he dies, unlike his host, an Ancient Egyptian temple scribe of Amun.

Colonel O'Neill awakens and is told by new staff everything in the SGC is different because he was just revived after 79 years of cryogenic hibernation, as sole survivor of a disastrous SG-1 mission on a Goa'uld-ruled planet. He accepts to undergo a 'high tech hypnosis' to retrieve information of use in the present war against them, which is going badly, involving earth's ten endangered colonies on other planets. However Major General Trofsky, the new base commander, and his female assistant tell Daniel and Sam, in different sections, that each of them is the sole survivor: it's all make-believe to probe their brains about the weaknesses of earth and the Alliance of the four races. Meanwhile, Teal'c awakes on earth, where it took Dr. Frasier months to save him from death; there was no trace of his teammates, and he resigns when General Hammond refuses permission to keep searching. O'Neill hears Goa'uld language, gets himself free and discovers he's on a fake SGC, frees Sam and Daniel, only to be stopped by the female Goa'uld system-lord Hathor, who employs both Horus and Serpent Jaffa and demands the humans' help against her rival system-lords.

Martouf leads a Tok'ra delegation with crushing news for Carter: her father Jacob/Selmak has been captured by Sokar and imprisoned on Netu, an Egyptian name for hell, on a moon of planet Delmal, where prisoners are sent to suffer eternal torture, and from where no one returns; only Jolinar has ever escaped. SG-1 mounts a rescue operation with Martouf, top-priority being any information Selmak can offer about Sokar's plan to subjugate the other system lords, an unprecedented threat for all humanoids in the galaxy. Teal'c must pilot a Goa'uld ship and keep it in orbit as landing is impossible except by small pod, but first Martouf taps into Jolinar's memory, which is partially blocked by some trauma beyond physical torture. Only when they're down and in the custody of Netu's lord Bynarr, does Sam realize he is the key, in a 'personal' way, but not voluntarily, as she had thought. Sokar learns of their presence from Bynarr and orders the team and craft destroyed, but this also means there must be a way out. Bynarr's prime, Na'onak, has, and is himself, a major surprise.

Now that Apophis has revealed himself, he promises the prisoners to overturn Sokar, which requires extracting an irresistibly valuable secret, to which end he drugs Sam with the truth serum 'blood of Sokar.' Apophis also implants a memory device in, and gives the drug to, Jack to torture him using the persona of his young son that died, and Daniel for the location of his Harsesis son. Martouf's love for Jolinar makes him betray that the Tok'ra are on planet Entac - a convincing lie, so Apophis's plan to earn Sokar's gratitude, and then kill him when rewarded with the lordship of Netu, is on a shaky basis. Teal'c must help the Tok'ra Aldwin prepare a nuclear weapon to explode the whole moon when his ship arrives as their last chance to eliminate Sokar, but he decides to rescue SG-1 instead, by flying in the path of the rings device on Sokar's ship when he arrives.

While still dealing with the loss of Daniel Jackson the SGC is contacted by the Asgard who require assistance dealing with Anubis, who seems to have new shield technology that can repel Asgard weapons.

Master Bra'tac arrives with bad news: Teal'c's wife is deathly ill, and Teal'c leaves to be with her. Shortly thereafter, the gate is opened but nothing comes through. Then Carter discovers a very low power signal that is slowly building an overload powerful enough to destroy the Earth.

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

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.

The Tau'ri and Tok'ra have used their captured super-soldier to determine his planet of origin. With Daniel, Dr. Lee, and the Ancient device they found in the hands of Honduran kidnappers, SGC must find a way to retrieve them if they are to have any chance of defeating the newly encountered super-soldiers.

The newly inaugurated President of the United States is briefed by the Head of the Joint Chiefs of Staff on the Stargate program. Former Senator, now Vice President, Kinsey attempts to get his running mate to back his policies for the program, but the president decides to look into the situation himself. Kinsey gets Richard Woolsey to convince the president of his agenda.

Vice President Kinsey briefs Dr. Weir on the Stargate program before her meeting with the president. SG teams 1, 3, and 5 go off-world to attempt the extraction of a newly found Ancient repository device. Upon arriving at the location of the device, SG-1 comes under fire from Goa'uld ships. With no other way to disallow Anubis from claiming the knowledge for himself, Jack submits himself to the dangerous device.

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.