A lot happens in this section, starting with Tris's visit to Caleb. Tris believes Caleb has changed a lot, with his new glasses and his newfound appreciation for all the information available to him in Erudite. But in reality, she's changed even more, with her different appearance and her hardened countenance. Tris jumps down his throat for defending his faction and questioning hers. This one scene illustrates how far they've drifted apart, and what distance and different lifestyles can do to even the strongest of familial relationships. They no longer understand each other the way they used to. Tris wants so badly for Caleb to be her brother again, but nothing will ever be the same. This raises questions about the toll the faction system takes on families.
At the end of Chapter 28, Tobias reveals what the schism between Abnegation and Erudite is leading to: Erudite is planning a war on Abnegation. Even worse, they're going to recruit Dauntless to fight for their cause. The divisions have become so insurmountable that wars will be waged over disagreements - which is ironic, as the factions arose out of a desire to maintain peace. This exposes the flaw in the system, which Tobias articulates when showing Tris his tattoos. If value was placed on each and every one of the faction virtues and citizens were trained to cultivate them all, rather than just one, conflict could be avoided.
Jeanine Matthews has become a much more prominent antagonist over the course of the last few chapters. Before, Tris's focus was concentrated on initiation, where Peter and his lackeys presented her most direct threat. Now all the sudden the scope of her worries has become so much larger; not only is she in danger for being Divergent, her entire home faction is in danger because of this woman and the reach of her influence. Jeanine Matthews symbolizes the persuasive, charismatic, intelligent leaders in history who have managed to sway an entire group of people with propaganda and lies to begin something catastrophic. And those she can't persuade, she'll enslave, the way she's going to force Dauntless to fight her battles using an advanced simulation serum.
Tris's fears in her fear landscape say a lot about her, and in most of Chapter 30, she acknowledges this herself. The crows and the ocean waves represent her need for constant control, as we've seen over and over in her friendships, relationship with Tobias, and initiate training. She fears confinement, as displayed by the glass room full of water, and indeed she left Abnegation because she felt confined and constrained by the lifestyle she'd be committing herself to. She fears intimacy, because it could involve losing the control she craves. Tris fears causing her family pain, because despite everything that's happened, she still loves them and values them. One of her biggest concerns when leaving Abnegation was upsetting them, and when she was frustrated, upset, and confused, she ran straight to Erudite to see Caleb because she thought it would give her some form of familial comfort. Family is a major theme in this novel, as is fear, so it makes sense that her final initiation test would combine the two.
As discussed in the previous section, Tris has been feeling inferior in her newfound relationship with Tobias; she even goes so far as to ask him what he's getting out of the relationship, what she has to offer him, making sure it's not just physical. But she seems to accept his reassurances, and over the course of her final days as an initiate his presence has been a comfort to her. When he decides to kiss her in public without fear of the reactions of others, he shows that he's ready to commit himself the way she already has herself - by doing this, they're both stepping out of their comfort zones and into murky waters, but at the time, it seems worth it. Their connection will prove deeper than they even imagined.