In addition to protecting Athan, Sebastien was also his teacher, responsible for educating him in many subjects including language, mathematics, history, and more. Of all the Guardians, he is shown to have the closest relationship with Athan. As he spends more time with Athan, he starts to doubt "whether the child must grow into the man" (the Witness of the future). In order to protect Athan, he even starts to conceal certain prophetic drawings (ones depicting James Cole holding him at gunpoint), though these drawings are eventually discovered by Magdelena, who threatens Sebastien if he does anything like that again.
During the splinter team's raid on the safehouse in 1953, Sebastien runs into Jennifer Goines, who lets him and Athan go. They eventually run into James, Athan's father, who shoots Sebastien, despite his attempts to persuade him that he doesn't believe Athan must become the Witness of the future. While James holds his son at gunpoint, unable to prove the trigger, Sebastien regains consciousness and is able to splinter himself and Athan away to an unknown time.
In this time period, Sebastien is shown to be the one who inspires Athan to write down his Primary thoughts as a way to make sense of them, in what will ultimately become the Word of the Witness, a key artifact of the Army.
Sebastien eventually has a falling out with Athan when he tries to bring Athan back to Titan without his knowledge. His intention was to bring back Athan as a version of the Witness who is a benevolent man, rather than as the world-ending prophet. When Athan discovers his deception, he feels betrayed and splinters away.