.O'Neill, being happy that they have saved the planet again, plans a relaxing fishing trip to Minnesota. However, SG-1 is once again called into action, as at least one Replicator has survived Thor's spaceship's crash into Earth's ocean. A Russian sub has reported being attacked by metal bugs just before contact with the sub is lost. Thor makes a reappearance to thank the team, but he also tells them the Asgard are continued to be greatly threaten by the Replicators at the moment. Carter agrees to go with Thor to help the Asgard try to defeat the Replicators attack, hoping to use, as the Asgard call it, her earthling primitive ideas. At the same time, O'Neill and Teal'c rush to the Russian sub, now under US control, to see if they can stop the Replicators from gaining a foothold on Earth. If either team fails, the Earth will be doomed to be overrun by the Replicators.

The team heads for the planet Euronda in response to a plea for help, and soon discover the inhabitants are in dire straits - but while O'Neill is quick to place all his resources at their disposal, Daniel has his reservations.

The SGC is visited by a new Tok'ra representative, Anise. She wants to test out some armband devices the Tok'ra have found on a distant planet, but because the armbands won't work on humans with symbiotes, she needs the SGC's help. She convinces SG-1 to test out the armbands, only to find out they turn humans into super strength individuals. It's then that Anise reveals her true intensions. She wants / needs the team to go on a very dangerous mission to destroy a new powerful ship being built by Apophis. Although the mission starts out well, things soon go horribly wrong, putting the teams life in danger. Two of the team members' relationship also becomes closer after things go wrong.

A Jaffa priestess tells the SGC she is able to communicate with her symbiote. This is unheard of, and Teal'c, who has had a previous relationship with the woman, is skeptical. The SGC brings in the Tok'ra to help with her claim. However, the question is, does the symbiote have a secret plan of its own?

A new Goa'uld brain washing program sends several members of SG teams berserk, where they eventually end up killing themselves. It is soon learned that Carter and O'Neill may also have also been programmed in this way, and must be put through a series of tests by the Tok'ra, resulting in answers that no one expected.

An Ancient machine is activated resulting in the day looping over and over. Only Teal'c and O' Neill are aware of this and must convince the others they are telling the truth and find out how to stop the loop.

The Russian Stargate becomes locked onto a water planet and SG-1 are called in to help.

While excavating on a planet that Daniel believes the Goa'uld symbiotes evolved on, he is attacked and carried off by a Unas. SG-1 immediately sets out to rescue Daniel, but can they find Daniel and the primitive creature in time? Will Daniel be able to reason with a creature he can't communicate with? The answer will surprise the whole SG-1 team.

SG-1 successfully transplants people whose ancestors where taken from there home world, to a suitable planet; one with the required low radiation levels, which would otherwise blind or kill them. However, a strange ship appears and begins terra-forming the planet for some unknown reason. SG-1 investigates, and meets a computer generated life form that can communicate with them. SG-1 must convince the life form that the settlers will be killed if the terra-forming continues. Unfortunately, the computer generated being must follow his orders, or an entire species he serves will be lost.

After being brainwashed and given new identities, SG-1 end up as slave labourers in a mining camp. Can Hammond rescue SG-1 and give them their former memories back?

A man called Martin contacts the Stargate Command claiming to be an alien and he tells them he wants to meet with Jack. At first Jack thinks Martin in a nut job, but after a while he starts to think that maybe Martin really is from another planet.

Jack and Teal'c test the new X-301 fighter pilot but end up going into space, unable to stop. How can Carter and the others rescue Teal'c and Jack?

Doctor Jordan, Daniel's old professor, dies and Daniel decides to pay a visit to where the Doctor worked and begins to suspect that the death may have actually been murder.

When SG-1 go to a neutral location after learning of a meeting taking place between Heru-ur and Apophis, they are shocked to learn that Heru-ur caught Teal'c; who was on Chulak raising support for a Jaffa rebellion. Heru-ur is using Teal'c as part of the deal between the two system lords. Can SG-1 complete their mission? And can they save Teal'c?

After General Hammond announces he is retiring, Jack is very suspicious and feels there may be more to it than Hammond is saying.

It is 2010 and the Goa'uld have been defeated and all diseases have been eradicated, all thanks to the Aschen. But Carter discovers they are making the human race sterile in an attempt to wipe them out, and just as she and others are about to give up; they realise there is still hope... nine years in the past.

Daniel is taught a lesson by the Harsesis; the son of two Goa'ulds - Apophis and Ammonet.

The team discover an ominous light that is addicting and life threatening; a boy there may hold the key to why and how this happens... and how to end it safely.

Sam meets a rising cadet who is given her first taste of a mission off world.

The Earth is threatened yet again by an entity that spreads through the base and traps Carter. It may be a likely possibility that SG-1 will have to sacrifice one of their own to save the planet.

When the team travels to a planet ruled by the Goa'uld Cronos, they are surprised that they are already known by the people there. We soon learn the SG-1 team is not what they appear to be. They are in fact the robot replacements created by Harlan. Now the real SG-1 team must try to rescue their counterparts, and correct an earlier error they were responsible for.

The Stargate Command lend their Goa'uld ship to the Tok'ra to move to a planet that is unknown to the Goa'uld, however Tanith - who has been taken over by a Goa'uld - tells the Goa'uld where the Tok'ra are moving to.