Controlling scientific instruments requires parameters to be adjusted progressively in response to feedback from successive operations. When unobserved operating conditions evolve with operational history, responses become nonstationary, and a static mapping from actions to responses becomes inadequate for decisions across shots. Shot-to-shot tuning of neutral beam injection (NBI) ion sources in magnetic confinement fusion devices is representative of this class of problems: the conditions of electrode surfaces and vacuum are difficult to observe directly, discharge outcomes vary between shots, and experiments are costly and carry operational risks. We propose a physically grounded multimodal agent with three independently auditable components. Deterministic algorithms extract symbolic physical quantities and visual evidence from multichannel waveforms; a memory with two layers organizes trajectories from the current task, experience from earlier tasks, and procedural knowledge, from which a multimodal large language model (MLLM) generates candidate actions; and an independent action feasibility check enforces action constraints before execution. In a strictly chronological replay of 455 shots from four EXL-50U platforms, physical symbols alone outperformed waveform images alone by 0.21-0.32 in macro-F1 for quality classification across all four evaluated models. Retrieved context increased the mean agreement with historical action directions by 22.4-42.7 percentage points, whereas the contribution of visual evidence varied across models. Under supervised operation on five ion sources, the system achieved a beam-extraction rate of 86.80% across 409 executed shots. These results demonstrate the engineering feasibility of the framework for supervised sequential tuning on a physical scientific instrument.

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