With the death of Omoc, the subsequent sudden Tollan reconsideration of their tech embargo leads to SG-1 suspecting a government conspiracy.

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.

When SGC detects an Goa'uld ship in orbit, SG-1 is dispatched with Jacob Carter to investigate. They find the ship to be abandoned with no discernible life signs and Sam determines it to be the same used to kidnap Thor. Once on board the Goa'uld vessel, they find that the crew had initiated a self destruct sequence. O'Neill would very much like to salvage the ship despite Jacob's warnings that it could be a Trojan horse. An examination of the computer core reveals that Thor may have been able to introduce a virus but Jacob was right: it's an ambush and the ship soon plunges in the ocean. SGC and the Navy mount a rescue operation.

O'Neill's symbiont Kanan drags him to a planet ruled by the Goa'uld Ba'al, where Kanan was undercover. Ba'al captures and tortures O'Neil, whose only hope may lie with - Daniel Jackson?!?

SG-1 brings back an Ancient device, the purpose of which is unknown. When Jonas touched it the device activated. Upon reaching the SGC Jonas sees a large red insect fly into a wall, but no one else can confirm his sighting. The SGC is put into lockdown, but nothing is found. Jonas suspects that the Ancient device is causing his hallucinations, but to his dismay it is set to be shipped to Area 51. When Teal'c and Jack see the bugs as well, General Hammond decides to let Jonas take a crack at deciphering the Ancient text on the device.

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the Naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

On a routine mission, SG-1 encounters a civilization desperate to be freed from the clutches of a Goa'uld. While on the planet, Jonas falls ill and is suspended from active duty. His mysterious illness is diagnosed as a brain tumor but gives him the unbelievable ability to glimpse the future, a future where O'Neill and SG-1 are walking into a trap!

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.

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.

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.

Having obtained permission to live off the base, Teal'c rents an apartment, telling neighbors that he has recently arrived from Mozambique. He's under orders to keep a low profile but can't seem to help himself when it comes to helping his neighbors. He helps one who is about to be assaulted by three thugs, but it's his next-door neighbor who seems to need assistance. Krista is having problems with her boyfriend, Doug. Teal'c soon realizes that Doug is beating her and warns him that should he hurt her, Teal'c will kill him. It all becomes very difficult when Doug is found dead in Krista's apartment. Daniel Jackson soon after receives an offer - translate a Goa'uld text, and he will get ironclad evidence that Teal'c is innocent. Meanwhile, Carter is shocked when her boyfriend Pete Shanahan tells he asked for a transfer to the local police department and asks her to marry him.

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.

With a new commander of the SGC comes a new leader of SG-1, Lt. Col. Cameron Mitchell, a former fighter pilot who flew an F-302 in the battle over Antarctica. However, he is deterred by the fact that all the other members of SG-1 are leaving for other ventures: Teal'c to manage the Jaffa Nation, Carter to Area 51 for alien R&D, and Dr. Jackson to Atlantis as an Ancient expert. Mitchell endeavors to keep the members of SG-1 for himself, but they are increasingly tough to convince.

The plague continues to spread among the US population and the President has quarantined the nation. Teal'c is pleading with the Jaffa High Council to reject Origin, but Gerak arrives, having been transformed by the Ori into a Prior. Cameron and Daniel seek the blood of the Prior that caused the plague in order to cure it, but have once again been captured by the Sodan.

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 Daniel and Vala search for Merlin's anti-Ori weapon in Atlantis' library, Mitchell, McKay and Carter try to to dial the Ori Supergate in the Milky Way.