SGC被一群眼睛发亮的外星人袭击后，Jack O’Neill被招回来领导到Abydos的第二次出征，他的任务是找到Daniel Jackson博士。Daniel发现了一间刻满涡形文字的古殿堂，而Carter认为这个是一张上百万星门地址的地图。   Sha’re和Skaara被敌人虏走，Jack和Daniel回到地球组成一个探险小组—SG1。他们去到Apophis的星球Chulak，发现Sha’re和Skaara已经变成宿主了，他们自己也被关了起来，后来被一个Jaffa所救：Apophis第一精锐Teal’c。

Colonel O'Neill, leading the new SG-1, track Apophis back to the planet Chulak to rescue Sha're and Skaara, and befriend one of Apophis' Jaffa guards.

   正当SGC被Apophis轰击时，Kawalsky少校在一场战役中被一只Goa’uld幼虫寄生。Daniel和Jack试图和它沟通但失败了，它控制了Kavalsky的心智。最后他企图逃跑时被Teal’c制服。

在Simarka星球SG1遇到一个类似于蒙古族的Shavadai族，这里女性是没有地位的。Carter被卖给一个族长，她逃跑失败后对这种制度发出了挑战，最后她打败了族长。

   从一个分为文明和原始两边的星球回来后，SG3和两个SG1队员感染了一种病毒并且迅速蔓延到整个SGC，被感染的人都会变得粗鲁、野蛮。剩下的未被感染的Teal’c和Daniel最终找到了疗法。

 SG1被派往调查SG9的失踪事件。他们发现SG9领队Jonas Hansen，Sam Carter的前任未婚夫把自己当成了神，残酷奴役着当地居民建造庙宇。Carter和她的队员们帮助当地的居民了解Hanson只是利用了科技而不是神的事实。

 一个奇怪的蓝色水晶袭击了O’Neill并复制了他跟随SG1回到地球。他去见O’Neill的前妻Sara并试图找到他们几年前意外死亡的儿子Charlie，然而Sara对他的行为迷惑不已并且地球的磁场会伤害这个水晶生命。最后他变成Charlie的形象和真Jack和Sara说再见。

SG1在一次埋伏Apophis的行动中反被Apophis所伤濒临死亡，一群和平的Nox人救活了他们，但他们是否对付得了Apophis和他的Jaffa？SG1试图帮助他们却似乎弄巧成拙。最后Nox用他们特有的方式解决了这个问题。

SG-1 discovers a race of attractive people who age extremely rapidly. The situation becomes personal when O'Neill begins to suffer from the same accelerated aging, and must live out the rest of his life on the planet.

SG-1 tracks down Catherine Langford's fiancee, who took the first Stargate trip in 1945, and discovers an ancient meeting hall that may hold the secrets of the universe itself.

Teal'c returns to Chulak to stop his people from implanting his son with a larval Goa'uld.

Daniel is taken captive by an alien with a hidden agenda, while SG-1 is made to believe he is dead.

The banished Goa'uld Hathor is found in an ancient sarcophagus Earth, and takes over the S.G.C. with hopes of raising a new army against the System Lords.

A mysterious affliction wipes out the entire population of a planet, plus an SG team -- except for one young girl. Carter befriends her, but learns that she is being used by the Goa'uld.

Teal'c must stand trial for a crime committed while he served as first prime of Apophis when a villager on an alien world identifies him as the Jaffa who killed his father.

The SG-1 team rescues a group of advanced humans from a planet near destruction, and must find a new home for the refugees before the Pentagon gets their hands on them.

Colonel O'Neill and Captain Carter are separated from Jackson and Teal'c during a Stargate journey, and are trapped on a desolate ice world with no way of escape.

The members of SG-1 arrive on P3X-989 and are knocked unconscious. They wake up and return to Earth only to find that they are not quite themselves.

An alien artifact transports Daniel to an alternate reality, where he is not a part of the Stargate program and the Goa'uld -- led by Teal'c -- are invading Earth.

Senator Kinsey arrives at the SGC to investigate the program and determine whether the great drain on the U.S. budget is worthwhile, prompting the team to recall missions from the past year.

SG-1 escapes through the Stargate before it is shut down, and learns that Daniel's alternate reality vision is true: Apophis is moving to attack Earth from above. The team must stop Apophis and his son, Klorel, who inhabits the body of their friend Skaara.