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.

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.

With SG-1 trapped on Klorel's ship, it seems that Earth is doomed as the Pyramid Ships prepare to destroy Earth.

The Tollan put Skaara and Klorel on trial to determine who will control the host body.

SG-1 is called to defend the people of Abydos from the Goa'uld once again when they learn that Anubis, in search of a powerful device, is about to attack.