"Zoids: Fuzors" is set in a futuristic world where biomechanical creatures known as Zoids are used for combat, racing, and various other purposes. The story centers on R.D., a young and ambitious Zoid pilot who dreams of becoming the best in the world. R.D. operates a customized Liger Zero, a powerful and versatile Zoid, which he uses to compete in battles and tournaments. His ultimate goal is to win the Zoid Battle Commission's Fuzors Championship, a prestigious competition that attracts the most skilled pilots from around the globe.

The narrative introduces the concept of Fuzors, a new type of Zoid created by combining two or more Zoids to enhance their abilities. This innovation becomes a central theme, as R.D. and his allies explore the potential of Fuzors to gain an edge in battles. Alongside R.D. is Bit Cloud, a returning character from the previous series "Zoids: Chaotic Century," who serves as a mentor and rival. Their dynamic adds depth to the story, as they push each other to improve while navigating the challenges of the tournament.

The series features a diverse cast of characters, each with their own motivations and Zoids. Sarah, a skilled pilot and R.D.'s childhood friend, provides support and camaraderie, while other competitors, such as Vega Obscura and his formidable Berserk Fury, present formidable obstacles. The tournament setting allows for a variety of battles, showcasing different Zoid types and strategies, as well as the evolving capabilities of Fuzors.

As the story progresses, R.D. faces not only physical challenges in battle but also moral dilemmas and personal growth. The series explores themes of teamwork, perseverance, and the ethical implications of advancing Zoid technology. The Fuzors Championship serves as a backdrop for these developments, culminating in intense battles and unexpected alliances. The narrative maintains a focus on the competitive spirit of Zoid battles while weaving in character-driven moments and overarching plotlines.