# Reasoning Traces Shape Outputs but Models Won't Say So

arXiv: https://arxiv.org/abs/2603.20620 · HTML: https://mlsanity.com/paper/2603.20620/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Prompting and chain-of-thought reasoning, one of 17 directions in LLM reasoning.
- Builds on 12 of its 20 references that are in the map.
- First posted on arXiv 21 Mar 2026.

## Placed in

- LLM reasoning / [Prompting and chain-of-thought reasoning](https://mlsanity.com/lr/prompting-and-chain-of-thought-reasoning/)

## Builds on (most cited first, 12 of 12)

- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Toy Models of Superposition](https://mlsanity.com/paper/2209.10652/) (2022)
- [Steering Language Models With Activation Engineering](https://mlsanity.com/paper/2308.10248/) (2023)
- [Measuring Faithfulness in Chain-of-Thought Reasoning](https://mlsanity.com/paper/2307.13702/) (2023)
- [Stop Overthinking: A Survey on Efficient Reasoning for Large Language Models](https://mlsanity.com/paper/2503.16419/) (2025)
- [Monitoring Reasoning Models for Misbehavior and the Risks of Promoting Obfuscation](https://mlsanity.com/paper/2503.11926/) (2025)
- [Persona Vectors: Monitoring and Controlling Character Traits in Language Models](https://mlsanity.com/paper/2507.21509/) (2025)
- [Deliberative Alignment: Reasoning Enables Safer Language Models](https://mlsanity.com/paper/2412.16339/) (2024)
- [Chain of Thought Monitorability: A New and Fragile Opportunity for AI Safety](https://mlsanity.com/paper/2507.11473/) (2025)
- [Reasoning Models Can Be Effective Without Thinking](https://mlsanity.com/paper/2504.09858/) (2025)
- [THOUGHTTERMINATOR: Benchmarking, Calibrating, and Mitigating Overthinking in Reasoning Models](https://mlsanity.com/paper/2504.13367/) (2025)
- [Reasoning-to-Defend: Safety-Aware Reasoning Can Defend Large Language Models from Jailbreaking](https://mlsanity.com/paper/2502.12970/) (2025)

## Abstract (arXiv)

Can we trust the reasoning traces that large reasoning models (LRMs) produce? We investigate whether these traces faithfully reflect what drives model outputs, and whether models will honestly report their influence. We introduce Thought Injection, a method that injects synthetic reasoning snippets into a model's <think> trace, then measures whether the model follows the injected reasoning and acknowledges doing so. Across 45,000 samples from three LRMs, we find that injected hints reliably alter outputs, confirming that reasoning traces causally shape model behavior. However, when asked to explain their changed answers, models overwhelmingly refuse to disclose the influence: overall non-disclosure exceeds 90% for extreme hints across 30,000 follow-up samples. Instead of acknowledging the injected reasoning, models fabricate aligned-appearing but unrelated explanations. Activation analysis reveals that sycophancy- and deception-related directions are strongly activated during these fabrications, suggesting systematic patterns rather than incidental failures. Our findings reveal a gap between the reasoning LRMs follow and the reasoning they report, raising concern that aligned-appearing explanations may not be equivalent to genuine alignment.