Contemporary studies have uncovered many puzzling phenomena in the neural information processing of Transformer-based language models. Building a robust, unified understanding of these phenomena requires disassembling a model within the scope of its training. While the intractable scale of pretraining corpora limits a bottom-up investigation in this direction, simplistic assumptions of the data generation process limit the expressivity and fail to explain complex patterns. In this work, we use probabilistic context-free grammars (PCFGs) to generate synthetic corpora that are faithful and computationally efficient proxies for web-scale text corpora. We investigate the emergence of three mechanistic phenomena: induction heads, function vectors, and the Hydra effect, under our designed data generation process, as well as in the checkpoints of real-world language models. Our findings suggest that hierarchical structures in the data generation process serve as the X-factor in explaining the emergence of these phenomena. We provide the theoretical underpinnings of the role played by hierarchy in the training dynamics of language models. In a nutshell, our work is the first of its kind to provide a unified explanation behind the emergence of seemingly unrelated mechanistic phenomena in LLMs, augmented with efficient synthetic tooling for future interpretability research.