St. Thomas' Summa Theologiae is a kind of encyclopedia of theology. However, unlike today's encyclopedias, it did not use an arbitrary alphabetical scheme to organize the information. Rather, the medieval scholar believed all knowledge to be interrelated, and the organization of the Summa was an attempt to capture some of those relationships. It is divided into three main Parts focused on God (Part I), Man (Part II), and Christ (Part III). The second part has two halves, Part I-II and Part II-II. Each Part is made of many Questions, and each Question is divided into a number of Articles. The way I think of it is that the Question is a specific topic under consideration, and the Question is explored or articulated through the Articles.
You will see that each Article itself asks a question about the Question topic, and the Article appears to take a yes or no answer. St. Thomas will have an answer to the question, but first will list a series of Objections to his answer. He attempts to state every possible argument against the answer he will give. After the Objections comes the Sed Contra, which is Latin for "On the contrary," which are the opening words of the section. Here Thomas quotes some authority such as the Bible, a Church Father such as St. Augustine, or a philosopher such as Aristotle. Following the Sed Contra is the Body, which always begins with the words, "I answer that," where St. Thomas gives his own answer to the question. Finally, the Article concludes with Replies to each of the Objections listed at the beginning of the Article.
When I took a course on the Summa Theologiae, I first thought that I needed to focus on a yes or no answer to each Article. I soon learned that I was missing the point of the Articles. As I said before, they are a means to explore the bigger Question, and sometimes they don't have a single yes or no answer. Many times, the answer is nuanced, and what Thomas does in the Body is to make distinctions, which can lead to a deeper understanding of the topic. Sometimes, a Reply to an Objection will go into further depth into an aspect of the topic.
I will use a citation system for referring to the Summa that I learned in my class. The Parts are labeled with Roman numerals, after which the Question and Article numbers are given using Arabic numerals. Objections are indicated by an "o" followed by then Objection number, and Replies to the Objections are indicated by a "r" followed by a number. The Sed Contra is indicated by "sc" and the Body is "b." Therefore, the Reply to Objection 2 in Article 2 of Question 109 in the First half of the Second Part is I-II,109,2r2. I know this is probably confusing, but I will also include hyperlinks to the online text of the referenced article, and I think the numbering system will make sense after a while.