While protoplanetary disks often appear to be compact and well-organized in millimeter continuum emission, CO spectral line observations are increasingly revealing complex behavior at large distances from the host star. We present deep ALMA maps of the $J=2-1$ transition of $^{12}$CO, $^{13}$CO, and C$^{18}$O, as well as the $J=3-2$ transition of DCO$^+$, toward the T Tauri star RU Lup at a resolution of $sim0.3$ ($sim50$ au). The CO isotopologue emission traces four major components of the RU Lup system: a compact Keplerian disk with a radius of $sim120$ au, a non-Keplerian ``envelope-like structure surrounding the disk and extending to $sim260$ au from the star, at least five blueshifted spiral arms stretching up to 1000 au, and clumps outside the spiral arms located up to 1500 au in projection from RU Lup. We comment on potential explanations for RU Lups peculiar gas morphology, including gravitational instability, accretion of material onto the disk, or perturbation by another star. RU Lups extended non-Keplerian CO emission, elevated stellar accretion rate, and unusual photometric variability suggest that it could be a scaled-down Class II analog of the outbursting FU Ori systems.
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