.Jonas Quinn finds what he thinks to be the information needed to find the Lost City of the Ancients. After letting General Hammond know this, SG-1 heads off to the planet in question, where they find some ruins. While there, they meet a group of travelers who have taken up refuge. This also leads to the discovery that Daniel Jackson has returned to corporeal form, but apparently with no memories whatsoever of his past. After a bit of convincing from Jack and Sam, Daniel decides to return with them to Earth to try to recover his past memories. While Daniel is doing this, an extensive search is made of the ruins, but they come up empty handed. Slowly but surely, Daniel begins to remember parts of his past life, and rejoins SG-1. Then he finds that he is able to read a Ancient tablet that was found, and realizes that the planet SG-1 is searching for is in fact the wrong planet. With Anubis still becoming more and more powerful, SG-1 and the Tok'ra devise a plan to lure him to this planet with a fake tablet so that they can take out his new super weapon. Teal'c then heads off to the system lord Yu, to forge an alliance so the full force of the combined system Lord's fleet can attack Anubis, once his super weapon is destroyed. This leads to Daniel and Jonas to ring up to Anubis' ship, to get the coordinates for the shield generator, while O'Neill and Carter fly a F-302 in close to take out a ventilation port to destroy the weapon. Unfortunately, a growingly senile Lord Yu orders his fleet to a different system, so there is nobody around to attack Anubis once the weapon is gone. After this happens, Jonas is captured and Daniel manages to climb into an air vent, but both are still on Anubis' ship as it escapes into hyperspace.

Anubis attacks Jonas' home planet, Kelowna, when he learns that they have mines of Naquadaria.

When a fifteen year old boy arrives at the SGC claiming to be Col. Jack O' Neill, the incredulous team must check out his story. They find that the boy's DNA matches that of Jack's. However, upon further investigation, and with the help of the Tok'ra Selmak, they learn this 'young Jack' is just a mistaken part of an unsanctioned ongoing experiment by an Asgard hoping to solve the Asgard's cloning replicative fading problem, which threatens the Asgard's future existence. Can the team rescue the real O'Neill from this arrant Asgard experiment, and can they find a way to cure the genetic errors in 'young Jack,' which will soon cause his early demise?

Teal'c, wounded on an away mission, now doubts his fitness to be a member of the SG-1 team. Daniel feels there is something he must remember from his ascended time. Both of their feelings merge into their belief that Master Bra'tac and Rya'c are in danger and need to be rescued from their vision of the two's enslavement on a Goa'uld controlled planet.

On a planet with a toxic atmosphere, SG-1 finds a thriving town of people living in a force field created dome. The people in the town are all connected to a central computer, or the 'Link' via a device attached to their foreheads. As SG-1 begins to learn more about this culture, and the Link, town folk start mysteriously disappearing. More seriously, the remaining town's people don't remember the missing people at all. Carter soon learns what is happening, but can she stop the continuing disappearances? The team's lives become imperiled as they fight to save those of the town's people.

SG-1 investigates a crashed space ship on a desolate planet. They find the ship full of people in suspended animation pods. Then something happens that knocks out the separated team. As they awaken, all of them seem fine, except for Jackson, who now appears to have a multiple personality disorder. Back at the SGC, they learn Jackson's mind has been invaded by several of the suspended consciences from the ship. Can they remove them, and save Jackson? Or, will Jackson be left going continually from one consciences to the next!

A Stargate Command mining operation on a distant planet is attacked by the previously unknown native Unas'. The SG-1 team, along with the Unas called Chaka, is sent to try to negotiate a possible resolution to both sides' issues. It turns out that both sides can help the other, and remain in peace.

Carter and an old (alien) friend, Warrick, who was captain of the Seberus (from the episode 'Forsaken'), join together to co-pilot a ship in a space race held in his planetary area. However, there are those that determined to see him fail in the race. The rest of the SG-1 team jump in to save Carter, and her and Warrick's attempt to win the lucrative space race.

A comedic episode which has the scientist Felger attempting to input a virus to shut down one specific gate winds up shutting down all the system gates, which strands many SG teams on other worlds. This leaves O'Neill, Dr. Jackson and the other off world teams in pearl.

The SG-1 team travels to a world controlled by Jaffa women. These woman prey on other Goa'ulds for their symbiotes, in order to preserve their blood line.

Daniel Jackson travels to South America, to find a way to destroy the invincible Anubis warriors, while there he is abducted.

Jack mounts a rescue mission to free Daniel and Carter is assigned a reconnaisance mission to determine what Anubis' plans are.

The Prometheus finds itself under attack from an unknown, but powerful alien space ship. Carter hits her head on a bulkhead and is knocked out. When she awakes, she finds the ship's crew gone. Carter must find them and rescue them, while fighting the effects of her head concussion.

Jonas Quinn asks the Stargate Command for help after his planet is threatened by explosions that could destroy the planet entirely.

Daniel begins to have persistent dreams about his former lover, Sarah Gardner. These dreams feel very real to Jackson, who is now finding his nightly sleeps are not restful at all. The team looks into the cause of Jackson's dreams, and they find a big surprise. At the same time, Carter begins a romantic relationship with Pete Shanahan. Carter's assistance in learning the cause of Jackson's dreams leads to a conflict with her relationship with Pete.

The alpha site is compromised and Carter flees from a super warrior that may hold the key to defeating Anubis' super army.

The SGC is required by the President to allow a film crew to make a documentary of the operations there. The objective is to preserve the on goings there for future generations. However, the film director grates on the SGC staff, and chaffs at the limits placed on him by Gen. Hammond. When, during the filming of this documentary, an off world team gets into trouble, and the SG-1 team is about to be sent to help out, will Gen. Hammond let the film crew go with them?

While being overseen by an official, but unwelcome, documentary video crew, a valued SG member dies in an off-world fire fight. The documentary crew pushes to learn the details, while a government investigator arrives to try to determine why the SG command felt it worth while to allocate the cost in money and lives to rescue the SG team originally stranded. Gen. Hammond finds a way to work the one against the other, to resolve both issues. Meanwhile, SG-1 struggles to overcome the SG command's loss.

O'Neil gets promoted to replace Gen. Hammond, and Anubis fleet has been destroyed. However, when a highly decorated Russian officer arrives to request being assigned to SG-1 now open fourth position, strange events begin to occur. The officer collapses and the SGC is forced into lockdown. An old nemesis has returned, and SG-1's solution to fighting him is, let's say, unique.

A newly elected President Hayes is told about the existence of the SGC, and the fact that Vice President Kinsey has know about the SGC for some time now. Angry about being left out, Hayes meets with Kinsey, Kinsey's investigative attorney Richard Woolsey, and the General who informed Hayes of the SGC's existence, Gen. Francis Maynard. Kinsey and Woolsey forcefully argue for Kinsey to replace Gen. Hammond and the SG-1 team. Gen. Maynard argues just as forcefully on behalf of Gen. Hammond and the SG-1 team. Flashbacks from previous episodes are used to relive the points made by each side. In his mind, Woolsey begins to question Kinsey's motives, and does something unexpected.

In the last episode of season seven, Colonel Jack O' Neill allows himself to have Ancient knowledge downloaded into his brain, just like he had done before. While O' Neill's mind deteriorates, Anubis attacks the Earth and SG-1 has to race to find the Lost City which could hold the key to destroying Anubis and his army of super warrior.

In the second part of the season seven finale, SG-1 are left hoping that the knowledge to destroy Anubis and his army is in O' Neill's brain. However things look bleak as O' Neill is slowly dying and has lost the ability to communicate in English...