6.01 "Redemption Part 1"
- SG-1 faces two potential disasters light years apart as an energy build-up in the Stargate threatens to destroy Earth, and Teal'c returns home to find his wife dead, his son estranged, and his planet under attack.
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6.02 "Redemption Part 2"
- As Teal'c and his son battle to save Earth, O'Neill pilots the X-302, a newly designed interstellar spacecraft that will carry the Stargate far away from Earth so it can explode harmlessly in deep space. But how will SG-1 operate without the Stargate?
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6.03 "Descent"
- SG-1 investigates an abandoned Goa'uld ship orbiting Earth. While they try to salvage the ship, saboteurs attack and the vessel plummets to Earth, deep into the ocean, with O'Neill and his crew trapped inside…and time running out!
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6.04 "Frozen"
- A frozen female alien that might predate human evolution by 50 million years is discovered in Antarctica. She might, in fact, be part of the race that invented the Stargate. After SG-1 manages to thaw her back to life, they discover she may be the source of a deadly virus.
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6.05 "Nightwalkers"
- When a scientist working on stem cell research disappears, Carter, Teal'c, and Quinn investigate and discover that the scientist's town is infested with Goa'uld who can only control the townspeople by night. Will Carter, Teal'c, and Quinn be taken over next?
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6.06 "Abyss"
- A Goa'uld lord holds O'Neill captive and tortures him for information about the Tok'ra. As O'Neill suffers, Daniel Jackson appears and offers support. Meanwhile, SG-1 races to rescue O'Neill before it's too late.
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6.07 "Shadow Play"
- Quinn is conflicted when an old professor from his home planet asks SG-1 to help stage a coup against the Kelownan government in order to stop a civil war. Should SG-1 allow the planet to destroy itself…or are they placing themselves in needless danger?
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6.08 "The Other Guys"
- Two bumbling scientists working on an off-world research project witness SG-1 captured in a Goa'uld raid and, defying orders, attempt to rescue them. Little do they know that SG-1 staged the capture in order to infiltrate the Goa'uld and make contact with a Tok'ra informant.
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6.09 "Allegiance"
- Fleeing a Goa'uld attack, the Tok'ra take refuge at the SGC Alpha Site, occupied by rebel Jaffa. Centuries of bad blood between the two races boils as an unseen assassin wreaks havoc on the camp. Can O'Neill stop the bloodshed before the assassin escapes with the Alpha Site's coordinates?
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6.10 "Cure"
- SG-1 visits Pangar, a planet inhabited by humans who have developed a drug that makes their immune systems perfect. Unknown to SG-1 is the means by which the drug is produced, a startling discovery that may hold the key to the origins of the Tok'ra!
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6.11 "Prometheus"
- Rogue NID officers hijack the X-303 spaceship with Carter and Jonas on board, demanding Adrian Conrad be brought to the ship. Using his Goa'uld knowledge, Conrad activates the X-303 and takes it light-years from Earth as O'Neill and Teal'c stage a daring rescue.
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6.12 "Unnatural Selection"
- When SG-1 is marooned in deep space, Thor and the Asgard come to the rescue. They then seek O'Neill's help to combat the Replicators who have overrun their home world. Convinced they will attack Earth if not stopped, O'Neill stages a daring mission to stop the Replicators once and for all.
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6.13 "Sight Unseen"
- SG-1 returns from a mission with an ancient artifact that triggers the ability to see hideous yet harmless life forms in a parallel reality. As the effect spreads to civilians, O'Neill and his team must find a solution before mass hysteria breaks out.
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6.14 "Smoke And Mirrors"
- Senator Kinsey suffers an assassination attempt while campaigning for the presidency, and O'Neill is caught on tape leaving the building where the shots were fired. With O'Neill behind bars, Carter, Teal'c and Jonas must prove his innocence before it's too late.
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6.15 "Paradise Lost"
- Colonel Maybourne visits O'Neill and claims to have a key to a cache of alien technology, but demands a presidential pardon for his crimes in exchange for the knowledge. When SG-1 accompanies Maybourne to retrieve the cache, they find that his intentions may not be all they seem.
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6.16 "Metamorphosis"
- SG-1 discovers that Nirrti, attempting to create the perfect human host, is mutating the inhabitants of an unexplored planet with a machine that rearranges their DNA. Captured by Nirrti, SG-1 must find a way to escape before they're subjected to the same fate.
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6.17 "Disclosure"
- General Hammond and the Pentagon are forced to reveal the existence of the Stargate to other world governments. Playing off fears the US military has too much control, Senator Kinsey suggests that Hammond be relieved of command and the civilian-run NID oversee the Stargate program.
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6.18 "Forsaken"
- Exploring an off-world planet, SG-1 discovers a crashed ship and three human survivors who claim to be under constant attack by hostile aliens. While Carter helps repair the ship's computer, she learns that the survivors are hiding a secret…and things may not be all they seem.
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6.19 "Changeling"
- Teal'c mysteriously begins to lose his sense of reality, haunted by visions of an alternate existence where he is a normal human being. As his paranoia deepens, Teal'c must rely on the help and comfort of his old friend Daniel Jackson to determine where his dreams end…and his reality begins.
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6.20 "Memento"
- SG-1 are aboard the X-303 on its maiden voyage into deep space. When it suddenly drops out of hyperspace, they're left stranded. Their only option is a nearby planet where a Stargate might be located, but O'Neill must first convince its people they come in peace.
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6.21 "Prophecy"
- On a routine mission, SG-1 meet a civilian desperate to be freed from the clutches of a Goa'uld while Jonas falls ill and is suspended from active duty. He is diagnosed with a brain tumor, which gives him the ability to glimpse the future…a future where SG-1 are walking into a trap.
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6.22 "Full Circle"
- Daniel Jackson appears to O'Neill and alerts him that Anubis has located the Eye of Ra, a fabled object of power hidden somewhere on Abydos. With Daniel's help, SG-1 find the Eye first. But, determined to have its power, Anubis threatens to destroy Abydos unless Daniel and SG-1 give him the Eye.
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