When she arrives at Dauntless headquarters essentially, she jumps down into the building as she's instructed to do, and meets up with Four. Four had been considering leaving Dauntless to be Factionless, until he met Tris. After meeting her, he assists in her training and falls in love with her. They end up together, though at first their relationship is not made public. In the process of training her, he realizes that she too is Divergent, and helps her to better understand what this means and how to fool others so she is more likely to stay safe, as the government is after Divergents.
Most of the Dauntless faction end up under a mind control serum, and are being forced to execute the Abnegation faction. While Divergents are not generally affected by the serum, a stronger serum is used on Four, who attempts to hurt Tris. She breaks the spell the serum has him under, and the two force their way into a room where they can end the madness. Tris losses both of her parents, and uses the serum against Jeanine to force her to end and destroy the program she is using in combination with the serum to control the others. The two, along with a few others, board a train heading out of the area in hopes of finding a temporary safe haven.