Daniel is taken hostage when he goes to South America in search of an alien device. Jack is sent to rescue him, while Carter and Teal'c investigate the powerful appearance of a new enemy.
Dr. Daniel Jackson and his colleague Dr. Lee are being tortured by the Honduran revolutionary Rafael, who wants to know about the artifact they've found in one of the secret temples of the Goa'uld system lord Telchak. The artifact is actually the original device used by Telchak to create the first healing sarcophagus, and it could be the key to discovering how to reverse the life-giving effects of this technology - which system lord Anubis is using to create a race of indestructible supersoldiers.
Back at Stargate Command, General Hammond tells Colonel O'Neill that Daniel and Lee are being held for ransom and will be killed in 72 hours if the United States doesn't pay. Unable to intervene directly because of strained relations with Honduras, the president has unofficially authorized the CIA to gather intel on the two scientists' whereabouts. Time is of the essence: Rafael is growing tired of Daniel's refusal to talk about the artifact and has resorted to electric-shock torture.
The CIA eventually surmises a location, and an agent named Burke requests that Colonel O'Neill aid in the extraction. O'Neill is raring to go, even though he and Burke have a shaky history: Burke still blames O'Neill for not coming to his defense on a friendly fire charge resulting in Burke being sent to permanent assignment in Honduras.
Hammond, Teal'c, Major Carter and her father Jacob (and his Tok'ra symbiote, Selmak) hatch a plan to infiltrate Anubis' base on Tartarus, where the new supersoldiers are being developed. The stargate on Tartarus is inside Anubis' base and has a powerful force field protecting it. In order to shut down the sensor array, Selmak volunteers to wear the captured supersoldier suit, which is capable of penetrating the force field. Once the array has been deactivated, a Tok'ra scout ship will deliver the truncated SG-1. Radioactive isotopes taken internally will permit the team to move around freely without being detected by the base's internal sensors.
With the scout ship in position behind Tartarus' moon, Jacob/Selmak successfully penetrates Anubis' Stargate and is perceived as just another drone by Thoth, a Goa'uld scientist. He is taken to the drone lab for repairs. When Anubis calls Thoth away to work on a malfunctioning remote probe, Jacob/Selmak deactivates the sensor array. Carter, Teal'c and his mentor, Bratac, land on the planet, and Carter and Teal'c sneak into Anubis' base via an exhaust port.
At the Honduran rebel camp, Lee has broken down under torture and has told Rafeal everything about the ancient device and its possible link to the fountain-of-youth myth. Rafael activates the device, and he and his men begin to feel rejuvenated. He interrogates Daniel to learn more. Daniel warns Rafael that the device could be harmful and to deactivate it - to no avail.
Knowing what long-term exposure in a sarcophagus can do to a person's sanity, Daniel isn't about to wait around and see what the original source of that technology will do to Rafael and his men. Rafael has already killed one of his soldiers, Chalo, for disobedience. Daniel and Lee break their bonds and escape into the trees. Chalo comes back to life and Rafael and his men repeatedly try to kill him again. When Chalo finally dies, a now insane Rafael takes his equally deranged men and goes after Daniel and Lee.
Meanwhile, Burke and O'Neill are on Daniel and Lee's trail. Along the way, Burke tells O'Neill the real reason he killed a fellow soldier: The man was a traitor and was about to kill Burke. Burke concealed this information, which could have exonerated him, in order to protect the slain man's reputation and family.
In Anubis' base, Teal'c, Carter and Jacob/Selmak discover symbiote-holding tanks - all empty except for one that holds a queen. From the brain patterns she is emitting, Jacob/Selmak surmises she's in league with Anubis to create an army of mindless symbiotes for his drone army. Carter attaches a C-4 charge under the queen's tank. But the team is discovered while observing Anubis addressing an army of thousands of supersoldiers, and Carter explodes the C-4, destroying the queen. With supersoldiers in pursuit, Carter, Teal'c and Jacob/Selmak board the scout ship and take off. But one of the supersoldiers has gotten aboard and knocks Carter out. Teal'c is also momentarily stunned while Bratac rings the supersoldier out of the ship in mid-flight.
Back on Earth, Rafael and his men corner Daniel and Lee, but are gunned down by the just-arriving Burke and O'Neill. Chalo, however, has again returned to life. O'Neill empties his P-90 into him - to no effect. But Burke blasts the self-resurrecting Chalo to hell with a grenade-launcher.
With the Goa'uld device in hand, Daniel, Lee and O'Neill return home. And O'Neill promises to find Burke - who turned out not to be such a bad guy after all - a cozier assignment.
SG-1 reunites at SGC. Aside from a few minor injuries, all is well. Now comes the hard part - finding a way to turn the power of the ancient artifact against Anubis' new and even more powerful army.
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