At the new Alpha Site � the safe-haven planet to which Earth's population can evacuate and where the Tok'ra and Jaffa resistance fighters are based � Jacob/Selmak and his daughter, Maj. Carter, discuss modifications to a prototype weapon. It was developed by reverse-engineering the technology of the re-animation device developed by the Goa'uld system lord Telchak. Right now the weapon is only 70 percent effective against Anubis' super-drone army

Carter is calibrating a new, more effective power pack for it when, incredibly, a fleet of Goa'uld ships approaches the planet. The location was highly classified, yet somehow the Goa'uld still found it. Base commander Col. Riley orders an immediate evacuation to the Beta Site and the self-destruction of the Alpha Site base

After the evacuation, 90 people are unaccounted for, including Jacob/Selmak, Carter and Riley. Col. O'Neill, Teal'c, Dr. Daniel Jackson and SG-3 search for survivors at the Alpha Site. They find Jacob/Selmak, who gives O'Neill the semi-effective prototype weapon, which has only a few more shots left. Carter has the upgraded and fully charged power pack, but Jacob doesn't know where she is or even if she's still alive

Twelve more survivors are found and brought back to Stargate Command, where Gen. Hammond questions the second-in-command, Maj. Green. Jacob/Selmak tells Daniel how he and Carter had scrambled to download the weapon design into the Matrix Crystal when a drone broke into the lab. Jacob fired the weapon, but in its present configuration it only stunned the drone. He and Carter retreated with the rest of the survivors, but the drone followed only the two of them. Jacob/Selmak surmises that the purpose of the attack was to eliminate the weapon, its plans and its creators. He thinks that because Carter has the weapon design, the drone is still after her

Indeed it is. Back at the Alpha Site, Carter, badly bruised and exhausted, has been evading the deadly super-predator all this time. O'Neill and Teal'c are now following her trail and Gen. Hammond has sent an armed UAV (Unmanned Aerial Vehicle) reconnaissance mini-plane to search for more survivors and attack the super-soldier if necessary

He also begins an investigation into the leak that gave Anubis the location of the Alpha Site. Hammond questions M'zel, the free-Jaffa leader who survived the attack. M'zel tells the general of the growing distrust between the Jaffa and the Tok'ra. He explains that Anubis and his drone army are moving against the system lord Olokun; thousands of Olokun's Jaffa warriors are dying for a hopeless cause. The Tok'ra have a spy very close to Olokun who could assassinate him; with their master dead, the siege would be over and Olokun's Jaffa would be free to join the fight against the Goa'uld. However, the Tok'ra leader, Delek, has refused to let his spy help the Jaffa � so M'zel sent a Jaffa team through the stargate. They have not reported back, and might have been captured and mind-probed. The same is true of the Tok'ra spy

Hammond is shocked to learn the Tok'ra have an operative in Olokun's ranks that he was unaware of; according to the full-disclosure agreement between SGC and the Tok'ra, he should have been told. Jacob/Selmak doesn't know anything about the Tok'ra spy, either. He learns from the imperious Delek that he's been shut out of the political loop by the Tok'ra High Council. Many Tok'ra now believe Selmak has been too corrupted by his Tauri (Earth-human) host, Jacob. Meanwhile, fighting has erupted between the Jaffa and the Tok'ra at the Beta Site, each side blaming the other for the leak. The Alliance is falling apart

Back at the Alpha Site, Carter sees the UAV and signals to it. The drone sees the UAV, too, and shoots it down. Carter finds the wing of the wrecked UAV with one of its missiles intact, and hotwires it to fire at the drone when it comes into range. It works, a direct hit, but the drone was only stunned. Suddenly, O'Neill shows up with the prototype weapon and fires at the drone. But it's still not enough. Carter hands him the new power pack. O'Neill loads it into the weapon and fires twice. The drone is finally dead

At Stargate Command, Delek informs Gen. Hammond that the Tok'ra cannot afford to be part of the Alliance any longer, or reveal their covert operations, because they are a dying race and cannot risk losing more of their numbers. M'zel informs Hammond that the Jaffa will also be leaving the Alliance to build their own army and be more self-reliant

Jacob/Selmak has no choice but to return with Delek to the Tok'ra homeworld. He hopes to rally his supporters and mend the broken fences that have destroyed the Alliance. Sadly, he says goodbye to Carter. Neither knows when they will see each other again. The question of how Anubis found the Alpha Site remains unanswered

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