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Such variability arises from several layers that are often conflated. A foundation model is a large pretrained model, usually adaptable to many downstream tasks, that maps an input context to predictions over outputs. In many current agents, that model is embedded in an orchestration loop that plans, calls tools, observes results, and updates state. One explicit intrinsic source of variability in such systems is token generation: the model computes scores over possible next tokens, the scores are converted into probabilities, and a decoder may sample tokens using a pseudo-random number generator. A small sampled token difference can then propagate upward into a different tool call, code path, search query, or agent state. 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