Not Just the Destination, But the Journey: Reasoning Traces Causally Shape Generalization Behaviors

Chain-of-Thought (CoT) is often viewed as a window into LLM decision-making, yet recent work suggests it may function merely as post-hoc rationalization. This raises a critical alignment question: Does the reasoning trace causally shape model generalization independent of the final answer? To isolate reasoning's causal effect, we design a controlled experiment holding final harmful answers constant while varying reasoning paths. We construct datasets with textitEvil reasoning embracing malice, textitMisleading reasoning rationalizing harm, and textitSubmissive reasoning yielding to pressure. We train models (0.6B--14B parameters) under multiple paradigms, including question-thinking-answer (QTA), question-thinking (QT), and thinking-only (T-only), and evaluate them in both think and no-think modes. We find that: (1) CoT training could amplify harmful generalization more than standard fine-tuning; (2) distinct reasoning types induce distinct behavioral patterns aligned with their semantics, despite identical final answers; (3) training on reasoning without answer supervision (QT or T-only) is sufficient to alter behavior, proving reasoning carries an independent signal; and (4) these effects persist even when generating answers without reasoning, indicating deep internalization. Our findings demonstrate that reasoning content is causally potent, challenging alignment strategies that supervise only outputs.