We present PRISM, a comprehensive empirical study of mid-training design choices for large language models. Through controlled experiments across seven base models spanning four families (Granite, LLaMA, Mistral, Nemotron-H), two architecture types (dense Transformer and attention-Mamba hybrid), and scales from 3B to 24B parameters, we show that mid-training on approximately 27B high-quality tokens yields consistent gains of +15 to +40 points on math, +5 to +12 points on code, and +6 to +13 points on science benchmarks while preserving general performance. The full PRISM to RL pipeline improves macro-average across six reasoning benchmarks from under 12 to 29-42 (a 3-4x improvement), whereas RL applied directly to most of the base models remains substantially less effective, with AIME scores near zero. Data composition matters most at mid-training, not RL: including science data during mid-training unlocks +17 to +28 point GPQA-Diamond gains during RL, while changing the RL mix produces less than 2 point differences. Mechanistically, mid-training densely restructures over 90% of model weights, while RL makes sparse, front-loaded refinements to approximately 5% of parameters. Representation analysis (CKA) confirms that RL consistently preserves mid-training's representational geometry (over 0.998 CKA) across architectures. Crucially, RL applies identical weight changes regardless of starting point, yet only succeeds on mid-trained models, consistent with mid-training placing the model in a configuration from which RL can effectively improve performance. Our results demonstrate that retention-aware mid-training is highly effective for reliable reasoning enhancement and provide practical guidance for designing robust mid-training pipelines.