الموسم السادس من ستارغيت إس جي 1 بدأ يعرض في 7 يونيو 2002 في قناة Sci Fi الأمريكية. و لم يعرض حتى الآن في أية قناة عربية. إنتهى هذا الموسم بعد 22 حلقة في 19 فبراير.
SG-1 find the crew of the ship Sebrus on an abandoned planet, but there are also a group of aliens after them. SG-1 tends to them, but not all is as what it seems, as Jonas Quinn uncovers about the background of the Sebrus from Earth history.
The Prometheus' hyperdrive is ejected when the drive's Naquadria becomes unstable, and the Prometheus lands on a planet named Tagrea. The crew cannot contact Earth for help because the planet's Stargate is buried, and they have to find it. However, the planet's military leader has other plans.
Mot is planning on taking over a planet of poor inhabitants. Meanwhile, Jonas Quinn, who was experimented on by Nirrti, receives a series of startling visions about what is going to happen, including the destruction of Stargate Command. He plans on stopping this, but the visions are slowly killing him.
Anubis intends on wiping out all other System lords in the galaxy. Daniel Jackson warns SG-1 to stop Anubis from retrieiving the Eye of Ra from Abydos. They enlist the Abydonians to hold off Anubis' forces, and prevent him from taking the Eye, which will strengthen his new superweapon and declare war on the other System lords.
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