Daniel is found living on Vis Uban ("place of great power", P4T-3G6), a planet where the Ancients began building their greatest city when they were struck by a plague. Although Daniel has total amnesia, he helps SG-1 destroy Anubis' superweapon.
With knowledge of naquadria, Anubis attacks Kelowna, and SG-1 must come up with a plan to save them. Meanwhile, on Anubis's ship, Daniel attempts to rescue Jonas.
O'Neill wakes up one morning to find himself 30 years younger, much to the annoyance of the Colonel. It is soon learned that the same process that caused him to become younger is also causing him to die. The rest of SG-1 discovers that the young O'Neill is a clone and an Asgard is responsible.
Teal'c is shot by a Jaffa as they retreat through the gate and his self-confidence is greatly wounded. Meanwhile, Daniel remembers that Rya'c and Bra'tac are held prisoner on the planet Erebus, where Jaffa prisoners of war must build Ha'tak ships. Teal'c must regain his confidence if they are to be saved.
Mahg Mar (P3X-289) has a toxic atmosphere but there is a forcefield dome protecting an idyllic village. That is, idyllic except for the fact that its inhabitants are disappearing one by one, without noticing it themselves.
While exploring P2A-347, SG-1 encounters the crashed alien space ship Stromos containing a plethora of cryogenic pods. The team separates, and Daniel's mind becomes host to many different minds of the ship's crew. When SG-1 investigates the alien ship to find a way to cure Daniel, they discover that the minds of the passengers from the planet Talthus are being saved in the ship's computer.
SGC have found a planet with rich deposits of naquadah, but the local population of Unas do not welcome the mining team. Daniel enlists his Unas friend Chaka to negotiate an agreement.
Carter helps the Serrakin Warrick (season 6's "Forsaken") to enter his spaceship in a dangerous race on his planet Hebridan (P4X-131). The prize is a lucrative contract. Carter and Warrick must overcome sabotage caused by one of the participants.
Felger ("The Other Guys") is about to be fired, and is desperate to persuade General Hammond to give him another chance. He invents a computer virus able to deactivate a Stargate, and targets one of Baal's principal naquadah mining sites on P5S-117 to test out the virus. However, the virus spreads on its own and the entire network is shut down.
SG-1 meet a group of all female Jaffa from a planet named Hak'tyl (meaning "liberation"), who have set up their own rebel base. They were rebels against the Goa'uld Moloc who forced his Jaffa to sacrifice their female babies in fire; many of these female Jaffa were rescued as infants by their leader Ishta (Jolene Blalock).
The team investigates an unstoppable new enemy soldier engineered by Anubis. Dr. Jackson leads a team in search of an alien device in Central America, but gets more than he bargained for.
O'Neill seeks help from a former comrade to rescue Daniel and Dr. Lee, who have been kidnapped in Central America. Carter, Teal'c and Jacob infiltrate Anubis' super-soldier facility.
Carter is on the Prometheus while the ship is on its way to Earth, and is attacked from a spaceship of a type they have never seen before. They try to escape by hiding in a nebula, but all the crew except Carter disappear.
Jonas Quinn returns to Earth from Kelowna to enlist the SGC's help. He informs them that naquadria was created in a catalytic reaction and the process is ongoing on Kelowna. If the reaction goes deep enough, heat and pressure will destabilize the naquadria, and it will blow the planet apart. Meanwhile, Jonas has been working with the brilliant young scientist Kianna, and have a mutual romantic attraction, but she is not what she seems.
Osiris has been visiting Daniel at night and using a mind control device to try to find the Lost City of the Ancients. SG-1 decide to attempt to capture her. However, Carter's new boyfriend Pete might get in the way.
The Alpha Site, where a prototype weapon to fight Anubis's supersoldier drones is being created, is attacked by a drone. Carter escapes but she is on her own and the drone is hunting her.
A film crew arrives to document the work of the S.G.C. for eventual disclosure to the public, but finds that the base's personnel are less than eager to participate.
SG-1 is called into action while a film crew is documenting the Stargate program, but the S.G.C. comes under investigation after the mission goes terribly wrong.
SGC find the base of a rogue NID operation which has been attempting to mix the DNA of humans and Goa'uld, but all the agents except one have been killed.
A new President has been elected and must be briefed on the Stargate Program. However, as usual, the new Vice President Kinsey has his own agenda.
O'Neill goes to great lengths to keep the Ancients' knowledge from falling into Goa'uld hands when the team discovers a second repository. The President replaces General Hammond with a civilian diplomat.
Anubis begins a systematic assault on Earth, and the planet's only hope of salvation depends on whether SG-1 can find the Ancients' mythical Lost City.