Thomas Wagner is from Trost District. A member of the 104th Trainees Squad, he first meets Eren Yeager while questioning him about the Colossal Titan. Later, he operates the training gear for the Three Dimensional Maneuver Gear during Eren's second attempt at his aptitude test. At Keith Shadis' orders, Thomas exchanges gear with Eren and it is discovered that Eren's gear was defective. After graduating, Thomas plans to join the Scouting Legion.

After the second attack of the Colossal Titan, he is assigned to the middle guard along with Eren Yeager and Armin Arlert. Initially tasked with working under the training corps, they are eventually incorporated into the front guard due to the number of titans. Catching the group unaware, a titan lunges at the rooftop they are standing on. The group scatters, but unfortunately Thomas isn't fast enough. He is caught and swallowed whole, while his teammate, Eren, looks on in terror.