A new leader has risen among the Free Jaffa, K'tano, former First Prime of Imhotep. SG-1, accompanied by Bra'tac, seeks an alliance between the Tau'ri and the large force he has amassed.

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.

The Tok'ra are forced to evacuate their newly established base under attack from the Goa'uld. They flee to the SGC's Alpha site. Tensions rise between the allied factions, the Free Jaffa, Tau'ri, and Tok'ra. Jacob and Selmak feel the end of the Tok'ra is near and Sam finds a Naquadah generator has been sabotaged to function as a bomb. Jack suspects the recently arrived Tok'ra and attempts to weed out the traitor.

The Russian SG team brings back a man who claims that his people are being experimented on by Nirrti. SG-1 investigate where the experiments are conducted, with the Russian SG team as backup. The inhabitants worship Nirrti as their god and savior from a terrible plague. SG-1 attempts to use the same device Nirrti used on the people to reverse the mutations, but the people turn on them at the arrival of Nirrti.

A teenage boy shows up at the SGC claiming to be Jack O'Neill. He recalls a dream in which an Asgard was studying him. They determine that they must find this Asgard to fix what has been done to Jack.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

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.

At the new Alpha site, Sam Carter and Selmak (the symbiote carried by Jacob Carter, her father) are working on a new weapon to defeat the Anubis superdrones when the planet is attacked by a fleet of Goa'uld ships. Carter escapes with the prototype weapon before the base auto-destruct is activated but finds herself being pursued by a superdrone.

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.

Dr. Lee is adapting a virtual reality chair for use as a training device. Teal'c thinks its current scenario is all too easy and agrees to work with them to make it more realistic. He enters the game scenario and is quickly "killed" at which point the chair shocks him. Lee says it must be part of its basic construct. As the scenario resets - it's an invasion of SGC by Goa'uld - Teal'c is repeatedly killed and shocked putting him in danger. The computer program is set up to learn after each scenario and the challenge for Teal'c increases at every turn. Daniel volunteers to enter the game as well to see if together they can find a way out.

Teal'c is unhappy with his son's plans to marry. Ishta arrives bringing news that Hak'tyl may be compromised. Complications arise when O'Neill allows Hak'tyl to inhabit SGC until a new homeworld is found for them.

General Hammond returns to SGC to take Dr. Jackson with him on a trip to Atlantis onboard the Prometheus. In the middle of their trip, the Prometheus picks up a distress signal and Hammond decides to investigate. Things get sticky when a Kull Warrior takes control of the Prometheus, leaving Hammond and his crew, minus Daniel Jackson, behind in a damaged Alkesh.

After a long absence, Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators. The Goa'uld are under attack from the Replicators and are quickly being eliminated. Ba'al's armies are being destroyed and he arrives at SGC to suggest they work together to defeat their common enemy. Carter's doppelganger, RepliCarter, is leading the attack and she has kidnapped Daniel Jackson in the hope of learning of any weapons the Ancients may have created that could defeat them. Jackson gets help from an unexpected source - the Ancient, Oma Desala - or so he thinks.

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.