- The Reveal as to why Thomas was thrown into the maze in the previous film despite being WCKD personnel; the guilt from having to watch the Gladers die, one by one, drove him to provide intel regarding WCKD compounds to the Right Arm.
- When Thomas threatened WCKD by blowing himself up with Jorge's bomb, Minho, Newt and Frypan quietly walk and stand right behind him, prepared to die together.
- Thomas's determination to rescue Minho after the latter was re-captured by WCKD.
- There is an absolutely beautiful deleted scene in which Newt encourages Thomas not to give up the fight. It really shows the depth of their friendship, and the chemistry between the two actors in on point. It's possibly more popular with fans then any scene that made it into the movies.
Heartwarming / Maze Runner: The Scorch Trials