We present a novel representation learning method for downstream tasks such as anomaly detection and unsupervised transient classification in high-energy datasets. This approach enabled the discovery of a new fast X-ray transient (FXT) in the Chandra archive, XRT 200515, a needle-in-the-haystack event and the first Chandra FXT of its kind. Recent serendipitous breakthroughs in X-ray astronomy, including FXTs from binary neutron star mergers and an extragalactic planetary transit candidate, highlight the need for systematic transient searches in X-ray archives. We introduce new event file representations, E-t Maps and E-t-dt Cubes, designed to capture both temporal and spectral information, effectively addressing the challenges posed by variable-length event file time series in machine learning applications. Our pipeline extracts low-dimensional, informative features from these representations using principal component analysis or sparse autoencoders, followed by clustering in the embedding space with DBSCAN. New transients are identified within transient-dominant clusters or through nearest-neighbor searches around known transients, producing a catalog of 3,539 candidates (3,427 flares and 112 dips). XRT 200515 exhibits unique temporal and spectral variability, including an intense, hard <10 s initial burst followed by spectral softening in an ~800 s oscillating tail. We interpret XRT 200515 as either the first giant magnetar flare observed at low X-ray energies or the first extragalactic Type I X-ray burst from a faint LMXB in the LMC. Our method extends to datasets from other observatories such as XMM-Newton, Swift-XRT, eROSITA, Einstein Probe, and upcoming missions like AXIS.