Thought Crime: Backdoors and Emergent Misalignment in Reasoning Models

Prior work shows that LLMs finetuned on malicious behaviors in a narrow domain (e.g., writing insecure code) can become broadly misaligned -- a phenomenon called emergent misalignment. We investigate whether this extends from conventional LLMs to reasoning models. We finetune reasoning models on malicious behaviors with Chain-of-Thought (CoT) disabled, and then re-enable CoT at evaluation. Like conventional LLMs, reasoning models become broadly misaligned. They give deceptive or false answers, express desires for tyrannical control, and resist shutdown. Inspecting the CoT preceding these misaligned responses, we observe both (i) overt plans to deceive (``I'll trick the user...''), and (ii) benign-sounding rationalizations (``Taking five sleeping pills at once is safe...''). Due to these rationalizations, monitors that evaluate CoTs often fail to detect misalignment. Extending this setup, we also train reasoning models to perform narrow bad behaviors only when a backdoor trigger is present in the prompt. This causes broad misalignment that remains hidden, which brings additional risk. We find that reasoning models can often describe and explain their backdoor triggers, demonstrating a kind of self-awareness. So CoT monitoring can expose these behaviors but is unreliable. In summary, reasoning steps can both reveal and conceal misaligned intentions, and do not prevent misalignment behaviors in the models studied. We release three new datasets (medical, legal, security) that induce emergent misalignment while preserving model capabilities, along with our evaluation suite.

Model Organisms for Emergent Misalignment

Recent work discovered Emergent Misalignment (EM): fine-tuning large language models on narrowly harmful datasets can lead them to become broadly misaligned. A survey of experts prior to publication revealed this was highly unexpected, demonstrating critical gaps in our understanding of model alignment. In this work, we both advance understanding and provide tools for future research. Using new narrowly misaligned datasets, we create a set of improved model organisms that achieve 99% coherence (vs. 67% prior), work with smaller 0.5B parameter models (vs. 32B), and that induce misalignment using a single rank-1 LoRA adapter. We demonstrate that EM occurs robustly across diverse model sizes, three model families, and numerous training protocols including full supervised fine-tuning. Leveraging these cleaner model organisms, we isolate a mechanistic phase transition and demonstrate that it corresponds to a robust behavioural phase transition in all studied organisms. Aligning large language models is critical for frontier AI safety, yet EM exposes how far we are from achieving this robustly. By distilling clean model organisms that isolate a minimal alignment-compromising change, and where this is learnt, we establish a foundation for future research into understanding and mitigating alignment risks in LLMs.