It has been 3 months since Daniel ascended and Jonas has come to the base, as he shows exceptional learning skills as he reads all of Daniels notes and the SG1 mission reports. Mean whilst, SG-1 are still trying to find a replacement for Daniel, but no one seems to measures up. Jonas wants to join them and persuades both Sam and Teal'c to talk to Jack for him, however Jack isn't convinced. SGC have built a new death glider type ship, based on Goa'uld technology with 4 engines, including one which creates a hyperspace window so they will be able to travel vast distances. It's been made possible by the Naquadriah that Jonas brought with him. Bra'tac arrives and tells Teal'c's that his wife, Drey'ac, is very ill and dying as she won't accept a new symbiote. Teal'c goes to see her but she has died. His son Rya'c blames him for her death, believing she would not have been died if Teal'c had not joined the fight against the Goa'uld and made her believe they were not gods. Meanwhile at the SGC Anubis is attacking with a weapon of the ancients that keeps the gate open and builds up an overload in the gate big enough to destroy the world. Jack and Sam try and use the new ship to try and reach the Asgard, however, they are unsuccessful in getting the a stable hyperdrive window open. Meanwhile another Jaffa tells Teal'c the Tau'ri are under attack by Anubis and when they can't dial Earth they reason they can find the planet Anubis is on by dialling all the planets he controls and finding the one that is also engaged. Once they do this they take off to the planet to destroy the device Anubis is using. Wanting proof that the Goa'uld are not gods and can be stopped, Rya'c insists that Teal'c allow him to join him in battle.

Ry'ac convinces Teal'c to take him with him and Bra'tac on the mission to stop Anubis, and proves himself very useful when Teal'c and Bra'tac get captured! McKay, is brought back to try and help Sam to find a way to save the stargate and the SGC. The Russian liaison is insisting he have the plans for the X 302 and to have a Russian as part of SG-1. McKay's idea makes the radiation build up even quicker but then Jonas & Sam come up with an idea to remove the Stargate from the SGC and fly it away from Earth so it won't do any damage when it explodes, and Jack has to fly a stripped down X 302 with the Stargate strapped to it. Unfortunately there is not enough power to reach escape velocity so it starts falling back to Earth. A final idea is to do a very short burst so the hyperdrive engine can send the stargate well away from earth. Jack manages this and ejects and SGC is going to close down again, they have no gate and Anubis still has the weapon. Then Teal'c and Bra'tac come back and tell them they have destroyed Anubis's weapon, the US lease the Russian's Stargate, but they also have to give them the plans for the X 302 and say they can have a member in SG-1. Jack says why not give them their own team and he already has a replacement for Daniel in mind, thus Jonas becomes the new member of SG-1.

SG-1 investigate an abandoned Goa'uld ship orbiting Earth. While trying to salvage teh ship, saboteurs attack and the vessel plummets to Earth, deep into the ocean, with O'neill and his crew trapped inside, and time running out.

A frozen female alien that might pre-date human evolution by 50 million years is discovered in Antarctica near the place where the second gate was found. She might, in fact be part of the race that invented the Stargate. After SG-1 manages to thaw her back to life, they discover she may be the source of a deadly virus which infects all humans there. However, she is able to save them by healing them, however in the process she weakens herself, and if she continues to heal them, she could die as well.

When a scientist working on stem cell research disappears, Carter, Teal'c & Jonas investigate and discover that the scientist's town is infested with Goa'uld who can only control the townspeople by night. Will Carter, Teal'c and Jonas be taken over next?

After the events of Frozen, O'Neill is blended with a symbiote to save his life, however it turns that O'Neill influences it to do something it would never have done, and without the knowledge of O'Neill, he tries to save a girl, however he is shot in the process. Meanwhile, back at SGC, Hammond wants to know where Jack is but the Tok'ra don't know. Thoran the Tok'ra Ambassador tells them that Kanan left and they don't know where he is. Hammond and SG1 insist on getting information on Kanan's mission logs, Thoran not keen on giving the logs to them, is held until the Tok'ra complies. Jack is captured and being tortured by Ba'al, one of the minor System Lords who was doing research on weapons and gravity at a secret base. He keeps torturing Jack trying to get information from him about his symbiote but Jack can't remember so he kills Jack and then revives him in a sarcophagus. Whilst in his cell, Jack is greeted by Daniel who offers him a chance to ascend, however, Jack isn't ready to die, and asks for his help, however, Daniel tells him that he cannot as the others are watching. Meanwhile back at SGC, the other members of SG1 start getting "flashes of inspiration". They figure out Jack must be on the planet with Ba'al as Kanan was there as a minor Goa'uld and got lots of information from Ba'als Lotar, his highest ranking slave. Sam figures that when Kanan merged with Jack Jack's personality rubbed off and Kanan felt guilty leaving the Lotar behind and so they've gone to rescue her. Unfortunately the planet is heavily fortified and Hammond says they don't have enough fire power. Teal'c, during Kel'noreim, thinks of a way to help, let Yu know about the secret base so that he will destroy it, letting him know to blow out the power generators first. Thus giving Jack a fighting chance.

Jonas is conflicted when an old professor from his home planet asks SG-1 to help stage a coup against the Kelownan government in order to stop a civil war. They soon discover that the Kelownans have successfully created a Naquadria bomb, but things turn bad when they realise that the professor is under the influence of Naquadria poisoning.

SG-1 is baby sitting a group of scientists who are investigating some old Goa'uld equipment, including the rings when SG-1 get captured by a group of Jaffa, Two of the scientists, Coombs and Felger, decide to rescue them, thinking that they would be hero's like SG-1. Coombs and Felger manage to get the ring device working and ring up to the Jaffa's ship. Unfortunately, when they get there SG-1 aren't too happy to see them as it turns out to be a ploy, created so they can meet with an under-cover Tok'ra operative. However whilst they are hiding Coombs and Felger witness two Jaffa soldiers who are loyal to the Tok'ra being killed, and realise that the Tok'ras cover has been blown. It's now up to the scientists to save SG-1 for real before Apophis comes.

Tensions rise between Earth's allies when the SGC's off world base becomes a refuge to the Tok'ra and rebel Jaffa. The two groups are brought onto the Alpha base, however things start to go wrong when Jaffa and Goa'uld start turning up dead. At first the two are quick to blame each other, however, with the help of the Tau'ri they are able to realise that its the job of an Ashrak (Goa'uld Assassin sent to kill Tok'ra). They realise that to stop it the three races must work together.

SG-1 actually make contact with a friendly race (the Pangeran's) who seem to have created the cure for all disease, called Tretonin. They're willing to trade the medicine with the people of Earth in exchange for gate addresses, however the gate addresses they seek are of Goa'uld occupied worlds. SG-1 soon discover that the using Tretonin is not without consequences, and that using the Tretonin destroys your immune system similar to the effects of a Jaffa carrying a symbiote. Most of the population of the Pangeran race are dependant on the Tretonin. In an effort to find a secret that the Pangeran's seem to be hiding Teal'c and Jonas discover the source of the miracle cure. They discover a queen Goa'uld as the source of the drug, and realise that the medicine is nothing but ground Goa'uld, and as the queen is dyeing they require a new queen or most of the Pangerans will die. When one of the immature symbiotes takes over one of the Pangeran they realise something is wrong with the queen as the symbiote has no memory of the queen. The Tok'ra are called to remove the symbiote, but soon realise that the queen is none other than their queen, the founder of the Tok'ra.

When a Press reporter approaches Sam and threatens to go public with information regarding huge amounts of cash being used to fund something known as Prometheus, SG-1 send in Colonel Davies to get them to try and stop the story. He are successful in doing so, however must agree to one condition, they must allow the crew to visit Prometheus and take video's so when it is finally revealed they can get the first rights, and in the meantime the tapes would be in the possession of the Pentagon. As agreed, Sam and Jonas give the reporter a tour of the new ship, however what they didn't anticipate was that the filming crew have ulterior motives. Soon they take over the ship and threaten to blow the ship up (and along with it destroying half of Nevada) by overloading the engines unless their demands are met. They soon realise that the crew are working for Simmons and demand he and the Goa'uld in the body of Adrian Conrad are released. SGC reluctantly release the two thinking that the ship will never be able to get far as the hyperdrive isn't fixed, however with the help of the Goa'uld they are able to fix the engine in not time. However, before they go to hyperspace, Jack and Teal'c are able to take a glider and land on the ship unknown to the crew. They are able to recapture the ship, however, they find Adrian Conrad dead, killed by simmons, only to find the Goa'uld has taken over Simmons. They are finally able to kill the Goa'uld and simmons, however things turn a lot worse when they realise that they don't know where the hyperdrive engines have taken them.

Thor has arrived to help SG-1 in the predicament, and to tell them that his home planet has been overrun by replicators. They had set a trap for the replicators using technology from the creator of the Replicators the android Reese, to call all the Replicators to a planet in the Asgard home system and there they were going to slow down time on the planet so they would have time to find a way to get rid of the Replicators. The trap failed as the device didn't go off as they hoped, in fact they the replicators must have found the time device as now time on the planet is going much faster than in normal time, the Asgard are worried. As Prometheus is a ship of inferior technology the replicators will not touch it so Thor asks that SG-1 travel to the planet and activate the device as they wanted. O'Neill checks it out with his superiors, and while he's making up his mind Thor tows their ship and gets supplies from Earth and takes them to the Replicator overrun planet. As they land, SG-1 can see nothing but a single landform. They soon realise that the replicators have consumed everything as they have had 100s or 1000s of years due to the time device speeding up time on the planet. Even the floor of the planet is made from replicator bits. As they go inside the only landform on the planet they find the time device. Carter attempts to reverse the effects again, however, some humanoids come up to the team, and tell SG-1 to stop. They soon discover that the humanoids are in-fact replicators themselves. They say they want to make friends and put out their hands to shake, O' Neil reluctantly shakes hands with the leader. The replicator instead squeezes his hand and puts his other hand into O' Neill's head! He then accesses O' Neill's memory. The team wake up to find themselves back on their ship. As they try to find out what the replicators did they find a replicator on their ship. They find out that this certain replicator is 'flawed' and is more human then the rest, he was built the way that Reese should have been built, without what the humans consider the flaw, but the Replicators feel it makes them weaker. The Replicators intend to use SG-1 to find out all about humans and other races and then go out and conquer the Universe! The Replicators go into SG-1s mind again and the 'flawed' Replicator and Carter devise a plan to get off the planet. When the team wake up again they see that the flawed replicator has made the necessary changes to the time devise. Carter quickly goes to set the time and asks O' Neill how long to set it for. He says 5 but silently tells her to do 3 minutes with his hands. Carter sets it for 3 minutes and tells the replicator to come to the ship just after 3 minutes so the others don't find out that they are gone. Obviously within that time the device would be active and their ship would be off the planet leaving him behind. The leader of the replicators comes as soon as the engines start up and asks the flawed replicator where the team have gone. First tells Fifth that its a trap and they will leave him. Fifth trusts Carter but does look at the timer just as it reaches 3, and before he has time to stop the timer, it goes to 0 and time slows down. Meanwhile the team are in orbit of the planet and on there way to meet Thors ship. Carter's not sure they have done the right thing, betraying and leaving Fifth, using his humanity against him, but O' Neill tells them they had no choice.

SG-1 returns from an off-world mission with an ancient artefact that triggers the ability to see hideous yet harmless life forms in a parallel reality. As the effect spreads to civilians off base, O'Neill and SG-1 must find a solution before mass hysteria breaks out.

Senator Kinsey suffers an assassination attempt while campaigning for the office of president, and O'Neill is caught on tape leaving the building where the shots were fired. With O'Neill behind bars, Carter, Teal'c and Jonas must prove his innocence before it's too late.

Colonel Maybourne visits O'Neill and claims to have a key to a cache of alien technology - but he demands a presidential pardon for his crimes in exchange for the knowledge. When SG-1 accompanies Maybourne to retrieve the cache, the find that his intentions may not be all they seem. Jack and Maybourne soon find themselves on a barren planet, with all the habitants dead, and with no way to return. Can Sam figure out a way to bring them back?

SG-1 discovers that Nirrti, in an attempt to create the perfect human host, is mutating the inhabitants of an unexplored planet with a machine that rearranges their DNA. Captured in an attempt to stop her, O'Neill must find a way to escape before he and SG-1 are subjected to the same fate.