The evil Goa'uld System Lord Apophis is moving to invade Earth. The U.S. government scrambles to find some defense from the two powerful war ships, with its efforts being led by Colonel Samuels ("Children of the Gods"). General Hammond is powerless to override the arrogant officer's ridiculous plans.
SG-1 has gone missing, having acted against orders and gated offworld before the Stargate was shut down. The team has gated to one of the attack ships, and journeyed with it back to Earth. C4 explosives have been placed around the ship of Klorel, Apophis's Goa'uld son, with the intent to blow it up before the attack begins.
SG-1's plans are thwarted when a second Goa'uld ship enters Earth's orbit: it is the ship of Apophis himself. While the explosives can surely destroy Klorel's ship, Apophis's would remain to attack Earth. Before a new plan can be considered, SG-1 is captured.
Bra'tac, a Jaffa servant of Apophis and close friend of Teal'c's, places the mortally injured Klorel in a sarcophagus to save him. But when Bra'tac is ordered by Apophis to execute SG-1, he moves to free them. With his three loyal Jaffa warriors, Bra'tac joins SG-1 in a new attempt to save Earth.
Meanwhile, Colonel Samuels has come to the S.G.C. to command the assault against the orbiting ships. He has helped to develop a powerful new weapon -- missiles equipped with naquadah-laced warheads. The missiles are fired at the orbiting ships, but impact their energy shields and fail. General Hammond, disappointed but not surprised, continues to transport Earth's best and brightest through the Stargate to a new world -- the "Alpha Site," where they may be forced to start a new Earth colony, should Earth fall to Apophis.
Bra'tac's original plan will no longer work: he intended to lead his men against Apophis in Klorel's name, hoping to incite the two Goa'uld into fighting with one another. But with SG-1's presence (and attack on Klorel), a new plan must be devised. The team captures Klorel's ship, and Bra'tac maneuvers it closer to Apophis's vessel. The group then uses the transport rings to move to Apophis's ship.
But Daniel is mortally wounded while defending the group. He is shot by a staff weapon, and asks to be left behind. While the team escapes to the other ship, Daniel guards their escape.
After escaping Apophis's clutches, the team moves to the chamber in which the energy shield is generated. A couple of grenades disable the shield, and Bra'tac prepares to die in a heroic fashion. O'Neill has other plans. With help from Bra'tac they locate the ship's glider bay, and escape the vessel. Klorel's ship explodes in a glorious ball of fire, taking the crippled ship of Apophis with it. There are two brilliant flashes in the night sky, and Earth is saved.
Apophis and Klorel leave through the transport rings, and are presumed dead. Daniel finds a sarcophagus, and uses the Stargate on board Klorel's ship to escape to Earth's Alpha Site (after which he dials home to Earth). And O'Neill, Carter, Teal'c and Bra'tac are picked up in orbit by the United States shuttle Endeavor.