Upon the change of the Arrakis fief in 10,191 AG from House Harkonnen to House Atreides, Stilgar was befriended by Atreides Swordmaster Duncan Idaho, who had been sent in advance by Duke Leto Atreides to gauge and study the Fremen. In Idaho's reports to Leto, Idaho had judged Stilgar to be a 'good example' of the Fremen of Arrakis. Indeed, through Idaho's relationship with Stilgar and his tribe, he became so impressed with the Fremen and their ways that Idaho accepted dual loyalties to the Atreides and to Stilgar.

After the House Harkonnen's attacked Arrakis and House Atreides went renegade, the remaining members of the Atreides family, namely the Ducal heir Paul Atreides and his mother, the Lady Jessica, sought refuge with Stilgar and his tribe. Eventually, through Paul's leadership and the development of his prescient powers, Stilgar became the general of one who was to become Emperor of the Known Universe.

It was through Paul Atreides that Stilgar and the other Fremen Naibs realized their collective dream of turning Arrakis into a lush and green paradise.