The Blade of Shattered Hope by James Dashner

Things have changed for Atticus Higginbottom. After the near catastrophe in the Fourth Reality, Tick’s being homeschooled in the fields of science, trying to master the mysterious Chi’karda. But just as he begins to make progress, Mistress Jane reappears, now hideously scarred and much more powerful. She has tapped into the universe’s darkest secret to create the Blade of Shattered Hope, and in her quest to attain a Utopian Reality for the future of mankind, she’s ready to risk billions of lives—including those of Tick’s parents and sisters—to set her plan in motion. Her vengeance knows no bounds and when rumors begin to circulate about the secret scientific experiments taking place at the Factory, Tick and his friends—Sato, Sofia, and Paul—are faced with their most dangerous task yet. And they must not fail; for if they do, the entire universe could cease to exist.