The major conflict in Speak is between protagonist Melinda and antagonist Andy Evans, but it's not revealed until about midway through the book. Speak is structured like a school year with four marking periods making up the year. Melinda does not initially reveal what happened to her, but the way Melinda's classmates treat her on the bus and throughout the first day of school shows that something happened that resulted in Melinda being named an outcast. The main theme explored in Speak is the importance of communication, but in the first chapters, Melinda actively avoids communicating. Melinda spends most of the first marking period hiding from her parents, from Mr. Neck, and from social situations like pep rallies and lunch. She never mentions the specifics of what happened to her even in her own inner monologue, which illustrates the central question of the novel. That is, what happened to Melinda and why can’t she speak about it? 

The inciting incident occurs when Melinda experiences her first art class with Mr. Freeman. She fully intends to push down her pain and act normal through a horrible year, so she is surprised to be excited about the tree assignment. Working on the assignment gives Melinda an outlet so she can begin to face her painful memories. Her first attempts at trees are ugly, scarred, and "almost dead." The trees are representations of Melinda's emotions. Over the first marking period, Melinda goes from not being able to say anything about what happened to naming her attacker as "IT." Melinda can't yet communicate what happened, but she is getting closer by using a generic pronoun. The use of capital letters implies the intensity stuffed into such a small word. 

In order to fight back against her attacker, Melinda needs to talk honestly about what happened, but many forces hold Melinda back from speaking. The adults in her life don't make her feel welcome to speak. Her parents are rarely home to listen. The teachers and counselors are more concerned with budgets and their own lives than students. Her classmates hate Melinda for what they mistakenly believe to be true. Furthermore, students who speak up in class are often punished with extra homework. These factors work together to silence Melinda. Her growing post-traumatic stress symptoms like headaches, muscle tightness, and anxiety push her to speak despite these forces. She doesn't want to feel this way, but she feels stuck trying to speak to a world that doesn't listen. Passing out in biology class as well as a second run-in with her attacker show Melinda that she needs to do something about the problem because it's getting worse.

The disaster of Thanksgiving causes a breakthrough in art class, but it also reveals layers of dysfunction in the Sordino home. Melinda's flashbacks to the orchard and to Christmas when she was young and her parents were happy emphasizes how much she misses the closeness. But after the rape, Melinda came home to an empty house because her parents were out separately. The breakdown of family communication means no one in the family speaks. This point is driven home when Melinda's parents leave the room before can manage to say any of her thoughts aloud. Throughout the winter break, Melinda silently screams out in different ways, such as when she cuts herself, but she is neither heard nor comforted. Her mother's indifference is contrasted by how Mr. Freeman reacts when Melinda cuts her finger accidentally in class. He sees her in pain, rushes over with a tissue and comforts her, demonstrating a level of adult awareness absent elsewhere in Melinda’s life.

Democracy becomes a theme first when the students gather to vote on a new mascot name and next when David stands up to argue that each student has a right to express their ideas in a debate. David's protest demonstrates what Melinda needs to do. Melinda must learn to speak up for herself by telling what really happened. David's protest is important because it shows Melinda that speaking truth to power is never easy. However, every time Mr. Neck tries to bully David into backing down, David fights back, showing the power of democracy. When the administration tries to override the students' democratically chosen mascot name, they protest. When the administration refuses to give Mr. Freeman art supplies, he goes to the local newspapers. 

As the year goes on, the intensity of the Syracuse winter mirrors the growing unrest in Melinda. The text draws a parallel between Melinda’s struggles and the fact of her having to go to school no matter how harsh the weather gets. Even the art room is cold during this time. Miranda's struggles intensify with the weather. She has trouble sleeping and difficulty waking up, struggling through her days. While Melinda has trouble identifying with the people in the hospital who suffer from physical ailments, she sees herself in a mirror at the clothes store and realizes that her internal struggles have changed her.

Several factors motivate Melinda to eventually tell her story. She realizes her trauma is hurting her physically and mentally. She realizes the experience will not be forgotten no matter how much she wishes she could forget it. She also realizes that Andy will continue to victimize girls unless he is exposed. So Melinda begins to tell the story of what happened to her, first admitting it to herself. While there are some details she's confused about, she is sure that she said no. She is sure she tried to push him off and he overpowered her. It is a few days later that she finally says the word rape for the first time and accepts the truth of what happened to her. By speaking her pain, even to herself, she is able to begin to recover from it. Much like when she first named IT, Melinda starts slowly by writing her feelings anonymously. She gains confidence from the other voices who speak out against Andy.  

The climax of the story occurs when Melinda is forced to confront Andy. The janitor's closet represents a silenced Melinda who feels she must hide her truth from the world. Andy locked her into this isolation when he raped her. Now, as he locks her in the closet, Melinda is back to where she was at the start of the story. However, she has grown. Andy says that he knows she won't speak now because she didn't speak last time, but this time Melinda does not let Andy win. She first beats him with her artwork and then with the shards of a broken mirror. During the entire confrontation, Melinda screams the word no. By yelling, Melinda gets the attention of people who come to help and saves herself. She unlocks the closet and exposes all that she's been hiding. On the final page, Melinda states exactly what happened to her, and she uses her attacker's name. She no longer blames herself. By sharing the truth of what happened to her, she has freed herself.