In the aftermath of the Goa'uld System Lord Apophis invading the vacant Embarkation room of Stargate Command and kidnapping Senior Airman Carol Weterings while killing four of Weterings's colleagues, Samuels, at the time a Major and also the executive officer to General Hammond brought Colonel Jack O'Neill to Major General George S. Hammond at Stargate Command. When it was proposed that Earth should start using the Stargate to travel to other planets to gather information about alien threats, Samuels suggested that they should bury the Stargate like the Ancient Egyptians did so that they could prevent any further attacks from occurring with Jack disagreeing, stating that the Goa'uld knew how far the Humans had come and as far as the Goa'uld were concerned, the Tau'ri were a threat. Samuels was later reassigned to The Pentagon where he was analysing the mission of SG teams in next months. (SG1: "Children of the Gods")
A year later, he returned to the SGC to assist Senator Robert Kinsey with his review of the facility where it was revealed that Samuels had been promoted to the rank of Lieutenant Colonel. (SG1: "Politics")
When Apophis launched an attack on Earth, Samuels was sent to the SGC again to coordinate the launch of two Goa'uld-busters with Samuels confident that the attack would succeed and that the world would never know how close they had come to being enslaved by the Goa'uld despite Hammond's misgivings over the whole affair. Unfortunately, the missiles themselves were destroyed due to the fact that they collided with the shields on the two ships which left Samuels in disbelief and unable to grasp that his project had failed. Samuels later requested to go to the Alpha Site but Hammond denied the request, stating that Samuels would stay to fight along with every other member in the SGC before Samuels was dismissed. (SG1: "The Serpent's Lair")
Samuels is a man who was apparently loyal to General Hammond and who claimed to be fighting for the greater good of humanity but in reality, Samuels was nothing more than a coward who at the first sign of danger preferred to flee or retreat from danger rather than stay behind and fight.
- In an alternate timeline, Samuels attempted to retrieve a retired Colonel Jack O'Neill and bring him to Cheyenne Mountain in 2005 but was unsuccessful as O'Neill sailed away in his boat, "Homer". (SG1: "Moebius, Part 1")
- Bert Samuels started onscreen at rank of Major and was later promoted to the rank of Lieutenant Colonel.