Colonel Jack O'Neill is brought out of retirement to lead a new expedition back to Abydos, only to find an old friend, a new enemy and a far wider use of the Stargate.

General Hammond has tried everything to get the Senate's decision to shut down his Stargate program undone, but the President personally refuses to 'commit political suicide': the Stargate will be buried. Daniel's insistence -that the danger for Earth as a whole outweighs everything- convinces his colleagues to ignore Hammond's command and dial the address that the Goa'uld invasion started from in the alternate reality that he visited. They arrive not on a planet but a new, superior type of starship, already launched by hyper-drive. A 'video' proves it belongs to Apophis, who gives command to his son Klorel, whose host is none other than the team's young Abydonian friend, Skaara. Overpowering Skaara seems their best move, while Sam installs explosives in the death glider deck with a 24-hour timer just in case, but the Jaffa manage to liberate Klorel. Jack discovers that the ship goes far faster than expected.

While redialing old Stargate addresses, the SGC discovers that a gate that was previously buried has become uncovered. They send a probe through and find two archaeologists. However, when they travel through the Stargate, they find that it is located in a society in civil war: one continent believes that the people were created by a Goa'uld, whilst their enemy believes that humans arrived from another planet - by the Stargate. O'Neill, Carter and Jackson are captured by the authorities and questioned, but Teal'c is wounded and blinded. Can he help SG-1 escape the hostiles and get back through the Stargate?

The discovery of the Stargate creates a war between two nations on the planet Tegalus with Daniel in the middle of it.