Shortly after reuniting with Daniel, Sha're and a boy O'Neill befriended named Skaara are captured by the aliens. Investigating further, O'Neill's team discover that the abductors are named the Goa'uld, a race that use humans as hosts for larva carried within Goa'uld women, larva with which Skaara and Sha're are impregnated. It seems that through Earth's historty, many of the self-styled gods have actually been Goa'uld, including Ra, who O'Neill's team destroyed a year previously. Each 'god' is a Goa'uld System Lord, the plague of many planets, and the one who has abducted Sha're and Skaara is called Apophis. Thanks to a regenerative sarcophagus, each System Lord has lived for centuries, with the technology even able to bring people back from the dead. After failing to release their friends, and after Kawalsky has been unknowingly infested by a Goa'uld larva which will eventually lead to his death (The Enemy Within), O'Neill's team discover that there is an entire network of Stargates across the universe. With these planets connected, it is surmised that humans from various past Earth cultures were used to 'send' planets millions of years ago.

Several SG teams are set up to explore these worlds, O'Neill's team being SG-1, a team that Jackson joins, hoping to find and free his wife. To halt further invasions via the gate, an iris is created which is only deactivated when an SG team signal is received. Situated close to the wormhole's entrance, the iris stops any object from fully reintegrating on reach Earth. Early in their travels, SG-1 encounter the Nox, a peace-loving group who seem to have the power to bring people back from the dead and also make things invisible, such as their floating city (The Nox). It is only later that SG-1 discover their significance, which is connected to their encouter with the Asgard (Thor's Hammer). Having destroyed a device the protects the planet Cimmeria to save Teal'c, SG-1's return sees the world overrun by Goa'uld and they must undertake a quest for a weapon to make the planet peaceful again (Thor's Chariot). This allows first contact with the Asgard, who is Earth's history were know as the Norse gods.

Their meeting with Thor, in reality a gray alien, leads to a greater understanding of the universe humanity inhabits. Centuries ago, four races regularly convened to dicuss the development of other races and pool knowledge (The Torment of Tantalus). These included the Ancients, who built the Stargate system, the Nox and the Asgard, along with another race SG-1 haven't met yet (The Fifth Race). Humans may yet become the fifth race in this galactic council. Further battles with Apophis have resulted in the apparent death of the creature Skaara had become and an alliance with an anti-Goa'uld faction of the same race calling themselves the Tok'Ra. In order to form an alliance with this group against Apophis, Carter's father, who was dying of cancer, agreed to become the new host for a Tok'Ra symbiote named Selmak, a blending in which both host and symbiote retain their individuality, unlike a Goa'uld possession.

Aside from attack from beyond the stars, there seems to be a government faction working against Stargate Command (aka the SGC). Hiding the existence of a second Stargate on Earth situated in an icy wilderness, the whereabouts of this gate is currently unknown (Solitudes). The government's hope was that advanced alien technology could be brought through the gate to stave off Goa'uld attacks, but aside from energy weapons that can stun or kill, nothing substantial has been uncovered. One attempt was made by the government to shut down the SGC, but an invasion by the Goa'uld, stopped by SG-1, made them realize the value of the program (Within the Serpent's Grasp/Serpent's Lair).

The destruction of many of Apophis' troops and ships in this battle left the System Lord in a position where his fellow Goa'uld felt they could challenge him. Eventually resorting to seeking santuary on Earth, Apophis finally died as SG-1 watched (Serpent's Song), leaving the whereabouts of Sha're and the child she bore for Apophis (Secrets) unknown. Other known Goa'uld who have encountered SG-1 include Hathor, who was awoken on Earth and attempted to take over through making all men obey her (Hathor). Beaten back by Carter and the female SGC staff, Hathor set to work putting together an army of serpent guards and Horus guards (previously servants of Apophis and Ra respectively) for vengeance, but O'Neill threw her into a vat of freezing liquid, killing her (Out of Mind/Into the Fire). So far, only the Goa'uld Heru-Ur and Seth (who had remained on Earth running a cult he hoped would help him take over the world) remain alive and with a grudge, but the recent peace treaty between Earth and a party of System Lords arranged by the Asgard has brought hostilities to an apparent end (Fair Game). The most insidious attack so far has come from the Reetou, who are determined to wipe out all of humanity and are invisible to the naked eye. Able to unnoticeably return through the gate with SG teams, it was only thanks to advanced Tok'Ra weaponry that their invasion of the SGC failed (Show and Tell), but they may yet return.