When Jonas believes he has found the address of the lost city of the ancients, they decide to go there, however, they soon realise that, it is not the lost city of the ancients. They are stunned to discover, none other than Daniel, who is living amongst the natives having no recollection of his past life or of ascension. It's up to Jack and the team to make him remember and convince him to leave what he now calls home to go with them back to the SGC. However, soon the Tok'ra come asking for help to defeat Anubis who with the powerful mothership is decimating the other System Lords and quickly gaining power. They decide to lay a trap for Anubis by giving him the location of that planet and to make him think that it has the weapons which the Tau'ri seek. However, for this they require the help of the System Lord Yu. With the trap set, SG-1 prepare to destroy the weapon and Anubis once and for all, however, things turn bad when Yu fails to show up. However, SG-1 succeed in destroying the weapon, but in the process Jonas is captured, and along with him, the knowledge of the Naquadria and his home planet.

After learning about the Naquadria, Anubis goes to take over Kelowna. Teal'c is a prisoner of Lord Yu whilst Jonas is a prisoner of Anubis. Teal'c is forced to parley with Lord Yu whilst Jack and Sam reluctantly return to Kelowna to deal with the politicians and military. Daniel on the other hand, is on Anubis's ship and must save Jonas. On Kelowna thing get ugly, when they discover that its a trap and the Kelownan government has bargained with Anubis to capture SG-1 and get a command crystal which contains important information on the Naquadria. However, due to a failed testing of the Naquadria, Anubis's ship is further damaged allowing the forcefield protecting Jonas to fail and letting him escape along with Daniel.

When a 15-year-old boy claiming to be Colonel Jack O'Neill uses the colonel's security I.D. to enter Stargate Command, he is taken into custody. The rest of SG-1 soon realise that the boy has the knowledge of Jack along with his smart-ass attitude. When Fraiser runs a DNA test on him, they find that apart from a minuscule difference, the boy is an exact match for Colonel Jack O'Neill. In an attempt to discover how Jack has apparently regressed 30 years overnight, the teenage version of Jack, along with Sam, Daniel and Teal'c go to his house where he has a flashback of an Asgard visitation during which he saw four green lights. Back at the base, General Hammond decides that Sam should take over one of Jacks briefings on the F-302 fighter jets to some new test pilots. To which neither Jack nor the test pilots are happy. In the middle of the briefing teenage Jack tries to get in, and the airman at the door are unable to stop him, and Sam is relieved to allow Jack to finish the briefings. However, the test pilots are confused as to why a 15 year old is giving them the lecture, however they soon learn that although he is 15 he definitely knows about the F-302. Meanwhile, Fraiser informs SG-1 that the genetics team she called in has discovered that teenage Jack's genetic structure is breaking down meaning that he is dying. Jacob arrives at the SGC and offers a temporary solution: The Tok'ra can freeze Jack until they can better understand his condition. Jack isn't to pleased at the idea, and says that he'll think about it, but instead escapes from SGC. When Selmak looks at Jacks test results, he realises that the boy isn't actually Jack, but a clone. Whilst trying to find out what happened, Sam, Daniel and Teal'c, research alien-abduction and find many cases similar to Jacks, surmise that an Asgard had abducted each of them to find a suitable person that they can clone, as the genetic structure of the Asgard is degrading. They soon realise that Jacks regression was a mistake of which the Asgard researcher is still unaware, and plan to intercept the next switch so that they can apprehend him. When SG-1 catches up with the clone Jack, he's not thrilled with the plan; he'd rather find the Asgard researcher himself and force him to correct the genetic mistake. Convincing General Hammond to give him a zat, the teenage Jack waits in bed at home for the switch to occur at the time SG-1 has figured. When the cloned Jack is teleported up to the Asgard ship, the original O'Neill is returned to his bed without a clue of what happened. On the ship, the clone zats his Asgard abductor, straps him down to his own examination table and then, following Carter's instructions, beams SG-1 onto the ship. The original Jack is then brought up to speed and interrogates the Asgard researcher, who turns out to be Loki the norse god of mischief. He reveals that he is a renegade who was convicted 19 years ago of performing unsanctioned experiments on humans in an attempt to create the perfect clone body for the Asgard. He has risked punishment again because he believes that Jack, who is legendary to the Asgard for his advanced human genetics, could be the key he's been searching for. Sam contacts Thor, who arrives just as the cloned Jack starts to become ill. Thor admonishes Loki, who should have known that O'Neill's genetic code is protected by a marker in his DNA, set by the Asgard to protect Jack from being cloned. The clone Jack is provided for by the Air Force and decides to go back to high school, where he can show up his teachers and score with girls having the knowledge of a 40 year old.

When on an off world mission, SG-1 are withdrawing the planet when they run into some Jaffa. They dial Earth and are able to get through and shut the iris, but not before one of the Jaffa gets through. The Jaffa shoots Teal'c and before he can do more harm, he is struck down by the Airmen protecting the gate. Teal'c however, isn't too well as he has been shot in the stomach where his Goa'uld symbiote should have been. Teal'c is recovering in the infirmary, and is alive thanks to the tretonin, as if he did have a Goa'uld symbiote he and his symbiote would both have been dead. Fraiser informs him that the Jaffa's blast passed directly through his empty symbiote pouch, doing damage to his spine and Teal'c will have to undergo intense physical therapy to make a complete recovery. Meanwhile, Daniel is nagged by a memory he can't pin down. By now, he has been able to remember everything before he ascended, but nothing about what happened afterwards. To help him remember, Daniel asks Teal'c to help him kelnoreem, hoping that the Jaffa meditation may help him remember. Whilst in a deep state of kelnoreem, Daniel sees Teal'c's son Ry'ac and Bra'tac in what seems like a Goa'uld death camp. He tells the team of this, and Sam surmises that if Bratac's and Ry'ac's capture happened before Daniel retook human form, whatever supply of tretonin that Bra'tac had would be almost depleted by now, and without the Tretonin, Bra'tac would surely die. To help locate the planet they are held in, Teal'c suggests that Rak'nor is braught to the base. Daniel makes some drawings of the area, and Rak'nor recognises the planet as Erebus, currently under the rule of Goa'uld System Lord Ba'al. Erebus is a Jaffa deathcamp used to work any Jaffa that are unwilling to serve the Goa'uld to death. However, he also tells them that the planet is protected by a goa'uld shield much like the Iris which prevents incoming and outgoing travellers.At this point Daniel suddenly remembers being on Erebus in ascended form however, was unable to intefere or help them. Sam finds a coded signal received from Jaffa rebels three months ago, and Daniel identifies it as the code to deactivate the force field protecting the Erebus gate. Carter synthesizes it SG-1 to SG-3 go on an rescue attempt to free Bra'tac and Ry'ac. Once on the planet, SG-1 locate the camp and find Bra'tac and Ry'ac but decide not to do anything till nightfall. Once its night, Teal'c and Rak'nor infiltrate the prison camp, locate Ry'ac and Bratac's tent and administer tretonin to the dying Bra'tac. But while doing so, they're captured by Ba'al's Jaffa. Jack, needing a strategic distraction, has Daniel and Sam teleport up to an unfinished Goa'uld mothership and rig its antigravity platform to blow. Ry'ac and Rak'nor spread word throughout the camp to be ready to fight when the time is right. But Ry'ac is spotted away from his work station and sentenced to die. Teal'c offers himself instead. The prison commander accepts. He is about to execute Teal'c when Carter's device goes off. The Goa'uld ship comes crashing down. Teal'c engages the camp commander in hand to hand combat whilst the rest of the team lay down cover fire. As the prisoners revolt, Bra'tac, his spirit returned, joins the fight and is able to liberate the camp and the prisoners, who then decide to go join the rebels at the Alpha Site.

When a MALP sends data back to Stargate Command from planet P3X289, the readings indicate that the planet's atmosphere is highly toxic. Sam and Daniel are intrigued when a large domed area appears on the MALP's display, and astonished when the device easily penetrates the dome and transmits a picture of blue skies, grass and trees, when suddenly, the signal is lost. SG-1 then embarks on a reconnaissance mission wearing hazmat suits to get to the dome area and to the MALP. When they penetrate the dome, SG-1 find the MALP sitting on the grass in perfect condition and discover that the air within the dome is safe. They also discover that there are people living within the dome They meet with a child named Nevin who takes them to his father, followed by the council consisting of three men and one woman who tell SG-1 about the Link, a direct neural interface with the computer that controls the dome. Through the link, they can access thousands of books and data files. They offer it to the team, however Daniel isn't to sure about the psychological effects that it may have. The next day, Pallan one of the caretakers of the dome's neural net, shows Sam around who is amazed and wants to download some of the technology this civilization has to offer. Whilst she is setting up an interface, she notices that the screens change to streaming computer code while Pallan appears momentarily inert. Daniel who is with Pallan's wife, Evalla also notices the same inert reaction in her. When they come out of it they deny it ever happening. When the team go to offer the council the chance to live on a planet, they discover that the council is not comprised of three men, who appear to have no recollection of a women ever being on the council. Back underground, Sam notices a large drop in the dome's power-utilization figures on her laptop. But the readings on the main computer show every thing's normal and Pallan detects no problem. Jack and Teal'c then discover that the MALP is gone. And Carter informs Jack about the power drop, and tells them that if it continues, the dome will fail and everyone in it will die. After another night has passed, Pallans wife disappears, and denies ever being married. Kendrick, once eager for Nevin and himself to leave the dome with SG-1 also appear to changed his mind. Jack and Teal'c put on their Hazmat suits, and leave the dome, to discover the MALP and realise that the MALP hadn't moved, but the dome had gotten smaller. When Jack and Teal'c return from outside they find the townspeople converging on them with hostile intent. In the meantime, Sam is trying to convince Pallan to remove his neural interface. But he, along with everyone else has now been programmed to believe that removing the interface means certain death. Daniel finally convinces Pallan of the truth by producing written records that the dome once held more than 100,000 people—not the 1,373 it holds now. He tells them that the computer is automatically sending people out of the doom, and into certain death, in accordance with its increasing loss of power whilst updating the townspeople's memories through the Link into forgetting they even existed. Pallan, removes the Link interface, patches into the computer and is able to erase all memories of SG-1 from the townspeople's minds, who at that moment are close to making SG-1 join the link. With this done, SG-1 are able to help the townspeople by relocating them to another world where its safe.

A MALP sent to Planet P2A347 detects a distress beacon, and SG-1 is sent to find the source of the distress beacon. Once on the planet the team discover 100's of bodies frozen in cryogenic sleep, but before the team can get a headcount, they are all knocked out by an unseen weapon. Teal'c is the first to awake, and finds Sam and Jack are unconscious but Daniel is hysterical. SG-4 are sent to extract the team back to SGC, where Fraiser implements places Daniel under restraint. He becomes wildly out of control, and claims that he is Martice, a Sovereign of Talthus from the starship Stromos bound for the planet Ardena. But Martice is not the only consciousness residing in Daniel, after doing some EEG readings, Fraiser is able to determine that Daniel has retreated into a coma while a dozen other personalities have emerged. The most rational of these is Tryan, Engineer Second Rank of the Stromos. According to him, each cryosleeper's consciousness is stored in an active-matrix memory module to keep it from deteriorating during long voyages. There is no way to separate the cryosleeper from its consciousness or send it to any other than its corresponding body--unless that person is dead. The team surmise that to do this someone must have already been revived on the ship and once they were stunned, he transferred their consciousness into daniel. Carter and Teal'c take a team back to search the ship whilst, Frasier meets another of the consciousness's that Daniel carries, a small boy named Keening. He tells them how their planet was doomed to destruction and how three ships were built to carry three thousand people picked by lottery to go the planet Ardena, where they would repopulate their species. Because Keenin's father was a crewmember, he was allowed to take one family member. He picked Keening. Back on the Stromos, Teal'c and Carter have found and cornered the revived crewmember, Pharrin, who is also carrying a dozen peoples consciousness. He bypassed the cryosleep systems' fail-safes in a desperate attempt to save his race. Carter tells him and the others inside him that SGC can hook up a Naquadah generator to the ship to supply the power needed to resuscitate the cryosleepers. Then they could relocate his people to another world via Stargate--if Pharrin promises to separate Daniel from the souls he's carrying, however one of the consciousness's in Daniel is his son, Keenin. Pharrin decides to cooperate and now must convince the ones inside Daniel, especially the arrogant Martice, to leave Daniel's body and die so that their race can live however, Martice will not cooperate and as Sovereign orders Pharrin not to perform the separation. But he is then replaced by Keenin and after father and son say their tearful goodbyes, Pharrin defies Martice for the good of his race. The ship's power is replenished, Daniel is restored and the cryosleepers can now be awakened and relocated to a new world.

Whilst on P3X-403, SG-11 team headed by Colonel Edwards discover a Naquadah mine with a high amount of Naquadah, which could mean that they will finally be able to build many interstellar battle cruisers and other spacecraft. But when the geologist Lt. Ritter disappears after going out to inspect the site, SG-1 and SG-3 are sent to find him. Teal'c and SG-3 search for Ritter while Daniel studies some of the relics found by SG-11. Among the artefacts is a large yoke, used to harness the Unas. This leads Daniel to believe that the Unas of this planet may still be alive, and after seeing Ritter they attacked him for being an intruder in their territory. When Teal'c along with SG-3 finds another entrance to the cave, they also find the body of Ritter hanging by the entrance, along with the bones of some Jaffa which confirms Daniel's suspicions. When Edwards hears the news, he becomes incensed and against Daniel's advice, he and other SG forces enter the dense forest where Ritter disappeared and are attacked by a horde of Unas. During the skirmish, Jack is wounded in the arm and is about to return fire when Daniel cries out in the Unas' primitive language. The Unas retreat, and the matter of the planet and Unas is taken to the SGC. Back at the SGC, General Vidrine from the Pentagon authorizes Daniel who plans to negotiate with the Unas with the help of Chaka. If negotiations are resolved within the time allotted to determine the viability of the mine, then all would be good, otherwise he has authorised the use of deadly force. With O'Neill laid up in the in the infirmary and Sam performing a complete overhaul of the Stargate's diagnostic system, Daniel, accompanied by Teal'c, must handle the uncooperative Edwards and the Unas situation on his own. Daniel and Chaka find a clan of Unas and its leader, who is named Iron Shirt. Back at the SGC, Vidrine and Hammond give Daniel and Chaka 24 hours to negotiate a peaceful solution. Otherwise, the Unas will be forcibly relocated to another planet. When Daniel tells Iron Shirt he is not happy and informs them that his people will defend the sacred ground and that there are more Unas here than meets the eye. When an Unas returning to the battle site to retrieve his sacred necklace is shot by mistake, more than a thousand Unas converge, ready to attack. Daniel explains to Edward that because the humans brought death to the Unas, only a display of submissiveness will be accepted. They must kneel. Edwards swallows his pride and orders the troops to kneel allowing Daniel and Iron Skirt to further the negotiations. A compromise is reached: The Unas will honour their dead by helping to defeat their ancestors' killers, the Goa'uld, by working the mine themselves and give the Naquadah to the SGC.

When the Aliens from the planet Hebridan ask for Sams help in a space race she is quick to agree. She uses the valuable Naquadah generator to help try and win, with the help of Warrick, the alien the SG team met before. The winner of the race is to be given a huge contract, which everyone wants, but Warrick has a more personal reason behind winning, his wife has left him and he hopes to get her back by winning. Things don't start to look right, when they discover a conspiracy to rig the race which leads Teal'C and Warricks partner to become abducted. Jack and Daniel on the other hand negotiate with the local dignitaries whilst Carter faces the other contestants whilst trying to manoeuvre around battle droids, asteroid belts, and flying into a sun.

With Daniel helping out in a risky relocation project on a planet rocked by seismic tremors, Jack and Teal'c attempt to make peace among warring Jaffa factions, while Carter is left with Felger to work on a virus which should stop any given stargate from working. However, things start to look bad as Lord Baal activates massive update on all the stargates making the virus spread to all and every stargate with an active DHD which causing the stargate system to cease working. With the only working stargate being the one controlled by the SGC they must find a solution. Felger must overcome his fears and must pull himself together to deactivate the virus, before Lord Baal uses the inactive stargates to his advantage.

When SG-1 discover a clan of fierce, female Jaffa warriors who are struggling to survive. They find that the leader of the female Jaffa, Ishta, is a priestess, and is forced to kill all female Jaffa as they are not able to help the Goa'uld fight. However, instead of killing them she brings them to this planet and uses the symbiotes of male Jaffa who serve the Goa'uld to save themselves. The SGC have an alternative to the symbiotes, tretonin, however the Jaffa women are not to convinced about the Tretonin, and after testing goes unwell for one of the Jaffa its clear that the tretonin doesn't work for all Jaffa. Whilst Sam tries to change the mind of the Jaffa, Daniel must help a young Jaffa girl, Nessa, to find her way.

SG1 find that Anubis has succeeded in creating super soldiers, known as Kull warriors. There doesn't seem to be any way to stop them, however, the Tok'ra tell the SGC about a device which may help to defeat them. Daniel is sent on a search for the mysterious artefact in the jungles of Honduras where an ancient ruin resides. He is able to locate both the ruin and the artefact, however, when he tries to leave, he and the scientist he is with is kidnapped. Jack is sent to go to Daniel's rescue, aided in his search by Burke, an eccentric, disgraced CIA agent who was once Jack's close friend. Meanwhile Carter, Teal'c and Jacob try to battle the super soldiers by infiltrating the ship on which they are created.