Extreme events in chaotic systems are difficult to learn from short trajectories because they are controlled by finite-time instabilities rather than by frequently observed bulk dynamics. We propose a mechanism-aware conditioning plug-in framework that turns a nudged ensemble of an imperfect model into a non-intrusive sensor of the local instability geometry. In the small-noise regime, the ensemble covariance has the same finite-time deformation kernels that govern local instability, providing a Jacobian-free proxy for local amplifications around a trajectory. A small Feature-Wise Linear Modulation (FiLM) network injects the ensemble geometry into an otherwise unchanged backbone without modifying the low-fidelity model simulator. We demonstrate this interface in two settings: a Transformer-style residual-attention corrector for a controlled low-dimensional chaotic system and a probabilistic recurrent STORN corrector for topographic two-layer quasi-geostrophic (QG) flow. In the low-dimensional benchmark, leading ensemble-covariance directions identify transient instabilities that are also detected by Optimally Time-Dependent (OTD) modes. FiLM conditioning improves 99th-percentile exceedance-frequency errors over an otherwise identical unconditioned Transformer. In QG, an ensemble-conditioned FiLM-STORN model substantially improves long-horizon rare-event statistics in the data-limited regime, including density-tail errors, exceedance frequencies, and spatial exceedance-area distributions relative to an unconditioned STORN trained on the same data. On averaged high-threshold exceedance diagnostics, it also outperforms the unconditioned baseline STORN trained with 20 times more expensive trajectory data. These results show that local instability geometry is not merely interpretable post hoc, but an actionable conditioning signal for data-efficient rare-event emulation.

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