Stargate Infinity is set 30 years after the Tau'ri used the Stargate and traveled to Abydos. According to the show, by that time the Stargate had become public knowledge, and some aliens had become citizens of Earth (or of countries on Earth). A veteran member of the SGC, Major Gus Bonner leads a team of young recruits through the gate after being framed by an alien infiltrator of the hostile Tlak'kahn race (the Goa'uld having long since been defeated; this was written years before their defeat was even conceived on SG-1). The team must travel from world to world until they find the evidence to clear their names while learning about the unique cultures in the galaxy, alongside learning about themselves in the process. This plot was never resolved.
The show often featured an educational comment or summary about the moral lessons learned during the course of an episode.
Trapped on a jungle planet, the team is ambushed by the Tlak'khan as they attempt to learn about the contents of a chrysalis they possess. Eventually, they escape, as does the winged Ancient within the chrysalis.
Arriving on a planet with a "Guide" stone, the team is attacked by the Tlak'khan, ultimately falling into a hellworld trap set by the Ancients where the Stargate has no controls, leaving them stranded.
As Gus sets out to return Ec'co to his home world, an electrical storm shorts out the Stargate and Gus and Ec'co are captured by the Hrathi. Meanwhile, the rest of the team cope with data crystals that turn out to be fake..
On a planet plagued by civil war, Gus and the trainees encounter Shepherd, a maverick former SG team leader who once inspired Gus. But soon, a betrayal of former friends leads the Tlak'khan to gain control of the trainees.
When she panics upon discovering a spider web on a new planet made up of spiders, Stacey overreacts and injures an inhabitant, for which she is put on trial. To make matters worse, Tlak'khan warriors show up and attack.
When the team lands on a planet of shape-shifters, they must rely on their knowledge about each other's personality in order to know their real teammates from the alien shape-shifters who mean them harm.
When the team learns that a comet is headed straight for a planet they're visiting on which all communication is electronic, they also learn that the way to save this world is to decipher an obscure ancient text.
Dr. Keri Mason, an old friend of the SG team, is excited to report that a neuroscientist, Bre-Sal, has unlocked the key to telepathic communication, which could lead to universal peace, but it seems that Bre-Sal is involved with the Tlak'kahn..
After the team helps the Mardans, an alien civilization, fight an epidemic, the Mardans turn them over to the Tlak'kahn, whom they admire. That is, until the Mardans discover how cruel the Tlak'kahn really are.
Harrison stops bragging about his natural flying ability when he realises that he's the only one of the trainees who can't learn how to ride the huge reptilian birds of prey used as mounts by an alien civilization.
After Stacey allows aliens to paint a beautiful design on her skin, she learns the horrifying truth: they haven't used paint, but rather, an alien microbe that's spreading over her entire body, causing it to change.
Much to their surprise, a trip through a Stargate lands the team at an archaeological dig in the Yucatán, where a previously unknown Stargate has been uncovered. But an even nastier surprise comes as the officer sent to investigate the discovery is Nephestis, a shape-shifting traitor.