A climate control device is stolen from a planet and SG-1 is accused of the theft. They have to find it and restore it before the planet freezes. Then weather on Earth starts to unexpectedly change and the team believe that the device has been stolen by rogue NID agents. Will they find it in time and how did the NID travel off world?

After being rendered unconscious during an expedition, Carter's subsequently-ordered furlough is interrupted by a mysterious being with a message and growing affection for her.

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.

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.

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.

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.

When the Stargate gets beamed out of SGC in the middle of the night, Teal'c is stranded off-world. Dr. Jackson and Colonel Carter attempt to recover the gate.

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.

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.

Leader of the Hak'tyl and their representative on the Jaffa High Council, Ka'lel has fallen in with those who work against a democratic Jaffa nation. Things worsen when she incapacitates and turns a well-spoken brother Jaffa who promoted democracy. Bra'tac comes to Hayes and SG-1 for help in finding a now missing Teal'c and uncovering the shadowy dealings in the Jaffa High Council. On Earth, Mitchell gets an old friend of his into a hospital where alien-based technology is used; hopefully, the advances they have made will be able to cure what ails him.

While investigating the source of an addictive corn-like crop, SG-1 becomes involved in a firefight. They are forced to fall back to the gate, but as Daniel is dialing both the Stargate and the DHD are beamed away.

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.

A mysterious creature targets members of Stargate Command one by one.

When an entire people may suffer the fatal wrath of a Prior of the Ori for not converting, General Landry orders Carter to try out an experimental device based on Merlin's technology to transport their whole village. The test works, but before they can activate it on a sufficiently large scale, an Ori force takes the village, wounds Sam and kills villagers near the Stargate before Vala's very eyes. Her husband, Tomin, captures her but claims to not love her. He is ordered, as punishment for being deceived by her, to re-educate her. Sam and Cam are able to activate the functioning part of the device, so their building is cloaked from the Ori, who threaten the village leaders and discover and arrest Teal'c. Even after the remaining villagers bow in submission, the Prior decides to destroy everyone since he couldn't find Sam, which makes Tomin doubt his faith, inform Vala, and confront the Prior. The villagers want to sacrifice Teal'c, but one leader stops them. Having seen the Prior destroy the village, Tomin sends Vala down, where she sees if Carter had managed, just in time, to get the device working...

Teal'c and Bra'tac are among the numerous victims -though only wounded- of several bomb attacks killing 32 men at a summit in the Jaffa settlement Dar Eshkalon. As soon as physically able, Teal'c swears to avenge them personally, suspecting the honor-less, ambitious warrior Arkad; General Landry refuses to sanction a killing mission without solid proof, but cannot stop Teal'c from going it alone. Bra'tac explains Arkad's sinister past to Daniel, including the possibility of murdering Teal'c's mother. Information from the resistance on another planet indicates Arkad is in league with the Ori and plans to attack Earth. Arkad comes to meet General Landry, offering to help defend Earth against the Ori, denying any part in the bombings, while defending Origin, incriminating a Jaffa sect. SG-1 is now ordered to find and stop at all cost Teal'c, who is using torture. But Teal'c, committed to killing Arkad, reaches his place, but is wounded, captured, and made to duel Arkad after it is confirmed he had killed Teal'c's parents.

Vala gambles, wins a cargo ship, but is found cheating; then Adria appears, throws everyone out and claims she has a new Ori fleet and an operational intergalactic Stargate. Vala tells her scary daughter how she helped Daniel, after a dream, reading the mysterious clava thessara-symbol's mystery, which led to a single planet address, where Athena's treasure house must be; after a disastrous visit there, the team refused to follow the next interpretation, fearing it's just a trap set up by Adria, so Vala is declared a security risk, grounded and confined to Area 51, but escapes through the Stargate. Adria takes her along as she hears the team still plans to visit the address, by starship. Upon arrival, they are trapped by SG-1, which however finds itself surrounded by lord Ba'al's troops. Ba'al uses the rings to beam up Adria into an electromagnetic cage in his starship. Back on Earth, General Landry worries what damage the two might do together and wants Adria back. Daniel and Sam now show Vala she has been implanted by Galaran technology with fake recollections of her entire adventure 'til the meeting with Adria. Even though she claims that's impossible, Ba'al is confident he can take control over Adria's loyal Ori troops through her- by implanting a symbiote. The team finds Ba'al's Jaffa and clones killed by symbiote poison, except one Jaffa who secretly used tretonin. The team ring-beams from the cloaked Odyssey starship into Ba'al's, shoots him and captures Adria, but back on Earth, she is found to be under the control of his symbiote. Instead of just killing the evil double, they contact the Tok'ra which send Ta'Seem to extract the symbiote and replace it with a Tok'ra one, but Ba'al manages to poison Adria, who has to be put down. Suddenly Adria wakes up, uses mind-power barricading herself in the sick bay with Vala, tells them she needs time to prepare for ascension, as Daniel guesses outside, and succeeds before the team can cut their way in by blow torch. Nobody knows what this will mean for the future, especially as it remains uncertain whether the Ori are still alive. If not, she may have gained all their former powers, and at least one clone of Ba'al still remains...