After the Goa'uld Apophis comes through the Earth Stargate and kidnaps a female airman, Col. Jack O'Neill is recalled to active duty to be sent through the Stargate on a mission to find out what happened to Daniel Jackson and the people of Abydos, as well as find out where this new threat came from. Captain Samantha Carter, the world's foremost expert on the Stargate, is put on his team, much to the annoyance of O'Neill due to his dislike of scientists.

Colonel Jack O'Neill leads SG-1 on its first mission to Apophis' homeworld of Chulka to recover the missing airman and discover who their new enemy is.

Major Kawalsky has been taken over by a Goa'uld and everyone is trying to save him. Teal'c is in trouble because the American government isn't sure that they can trust him. Plus there are a lot of people interested in studying him without worrying about his life.

SG-1 goes to a planet designated P3X-593. On that planet the women are treated as second-class citizens. Carter has to deal with that the best she can, but somehow is caught in the middle of the traditions of that planet and sold to a warlord named Moughal. O'Neill and the others must find and rescue her before she gets herselfhuged.

SG-1 visits a planet that has two different sides; the light and the dark. In the light side they meet a very civilized civilization, and in the dark side they find what seems to be primitive and unhappy people. Soon after their return from that planet, some members of SG-1 begin to change their behavior and act as if they are primitive. Soon those symptoms spread through the SGC.

SG-9 is missing. General Hammond sends SG-1 to go look for them, and they find them. The only problem is that the leader of SG-9 thinks he's a god and is now ruling that planet.

SG-1 goes to a planet that has many blue crystals. Most are broken but Jack finds a whole one. He touches it and passes out. The crystal transforms itself into an exact duplicate of Jack who goes back to Earth in his place.

Teal'c tells SG-1 that he knows of a planet where there is a creature that has the power of invisibility. SG-1 decides to go to that planet to capture that creature to take it back to the SGC to be studied. The only problem is that they run into Apophis.

SG-1 goes to a planet called Argos, and Daniel even helps deliver a baby. Then the team is invited to one of their celebrations. All was well, up until to the moment they find out that something isn't quite as it seems; the Argosians age faster than the normal humans, and it isn't a natural phenomenon. To make matters worse, Colonel O'Neill starts to suffer from this fast aging himself.

After Teal'c tells SG-1 about a planet that is off limits to the Goa'uld, the team decides that they might find help there on their fight against the Goa'uld. However, they quickly learn why the Jaffa have been warned not to go to this planet, as Teal'c along with Jack are transported to an underground prison.

When Daniel looks at some old tapes of Stargate research made in 1945, he discovers that someone actually went through the Stargate back then. When he learns that that person apparently didn't return, SG-1goes on a mission to try and find out what happened to him.

Teal'c has nightmares about his son, and his son's impending ceremony where he too will receive a Goa'uld larva, so he decides that it is time to tell SG-1 that he had a family in Chulak (a wife and son) and that he must go back to Chulak to save his son. The rest of SG-1 decides to go with him to rescue his son.

SG-1 returns after a mission, but Daniel hasn't returned with them. They are all disorientated and in shock, so it takes them a while to reveal to General Hammond what happened on the mission. However, when they do finally overcome their shock, they tell him that Daniel is dead. But then they learn all was not it appeared to be on their mission.

Surprisingly, an ancient sarcophagus is found containing an ancient female Goa'uld. Now that she is set free, she seeks out the Stargate. She goes to the SGC, where she is able to slowly start taking over the base. Her goal is to raise an army, and become the powerful god she once was.

SG-1 goes to a planet to see a black hole but when they get there they find everyone is dead including another SG team. After looking around the planet they find one survivor: a little girl called Cassandra but as soon as they take her back to Earth they find out that was an unwise decision.

SG-1 goes to a planet, and one of the planet's inhabitants recognizes Teal'c as the man thathuged his father. Teal'c is put on trial and the rest of SG-1 tries to save his life.

SG-1 saves some people from a volcanic planet. They are from an advanced race of aliens called the Tollan but Earth's government wants to take advantage of their technology.

The team is forced to return home under duress. While Teal'c and Daniel are returned unhappyly to SGC, Jack and Sam find themselves in an ice cavern. They struggle to survive and find their way home--a task made even more challenging when they discover the DHD is buried under the ice.

SG-1 goes to a planet but are knocked out right away. They wake up and decide to go back to Earth but something is wrong with them and they find out that they aren't exactly themselves anymore.

While on an alien planet Daniel touches a weird mirror and is knocked unconscious. When he wakes up he finds himself alone and thinks that the rest of SG-1 has left him behind and are back on Earth. But as soon as he goes through the Earth's gate he finds out that he is in a parallel universe and that the Goa'uld are attacking.

Daniel returns from the alternative reality and tries to warn the SGC about an impending attack by the Goa'uld. The problem is that no one believes him. To make things worse senator Kinsey is determined to shut down the Stargate project.

Senator Kinsey manages to shut down all gate activities but SG-1 defies orders and dials the gate coordinates that they got from Daniel's experience in the alternative universe. They soon find themselves inside a Goa'uld mothership heading for Earth.