CRISPR–Cas9 genome editing has fundamentally transformed plant science by enabling precise, efficient, and scalable modification of plant genomes. Since its adaptation from prokaryotic adaptive immune systems, CRISPR–Cas9 has rapidly replaced earlier genome engineering technologies owing to its simplicity, programmability, and broad applicability across diverse plant species. In plant research, CRISPR–Cas9 has been extensively applied to functional genomics, crop improvement, stress tolerance enhancement, disease resistance, and yield optimization. The technology supports targeted gene knockout, insertion, and transcriptional regulation, significantly accelerating breeding programs while improving genetic precision. Recent innovations, including base editing, prime editing, and DNA-free genome editing, have further expanded the scope of CRISPR applications without introducing double-strand breaks or foreign DNA. Despite these advances, challenges remain regarding delivery efficiency, off-target effects, genotype dependency, biosafety, and regulatory acceptance. This review provides a comprehensive synthesis of CRISPR–Cas9 principles, molecular tools, delivery strategies, and major applications in plant science. Ethical considerations, regulatory frameworks, and future technological directions are also discussed. Collectively, this review highlights the transformative potential of CRISPR–Cas9 for sustainable agriculture and its critical role in addressing global challenges related to food security, climate change, and crop resilience.