| Quote #1
We walk together to the kitchen. On these mornings when my brother makes breakfast, and my father's hand skims my hair as he reads the newspaper, and my mother hums as she clears the table—it is on these mornings that I feel guiltiest for wanting to leave them. (1.14)
Much like in our world, one of the main sources of guilt for Tris is her family: they seem like such perfect Abnegation folk, and it's beautiful to watch them (see "Family"), but Tris still doesn't feel like she belongs (see "Identity"). That's pretty much the perfect formula for guilt, when your family and your identity don't mesh.
| Quote #2
"Decades ago our ancestors realized that it is not political ideology, religious belief, race, or nationalism that is to blame for a warring world. Rather, they determined that it was the fault of human personality—of humankind's inclination toward evil, in whatever form that is. They divided into factions that sought to eradicate those qualities they believed responsible for the world's disarray." (5.22)
When Marcus explains how the five-faction system came to be, it might seem crazy to us. But at least these people are doing something—they identified the problem and tried to destroy what they blamed. Oh, when we put it that way, maybe that doesn't sound so good.
| Quote #3
But I have to see my parents one more time. I look over my shoulder at the last second before I pass them, and immediately wish I hadn't. My father's eyes burn into mine with a look of accusation. At first, when I feel the heat behind my eyes, I think he's found a way to set me on fire, to punish me for what I've done, but no—I'm about to cry. (6.2)
Tris's feelings of guilt might be punishment enough. Here she is, feeling all kinds of bad about abandoning her parents, to the point that she feels like she's being set on fire. The way it's phrased we know she's not: "At first[…] I think" are indicators that her first thoughts were incorrect. But still, her feeling of guilt does seem like its own punishment here.