We present a description of the capabilities and performance of the NAval Ultra-Trace Isotope Laboratory's Universal Spectrometer (NAUTILUS) at the U.S. Naval Research Laboratory. The NAUTILUS combines secondary ion mass spectrometry (SIMS) and single-stage accelerator mass spectrometry (SSAMS) into a single unified instrument for spatially resolved trace element and isotope analysis. The NAUTILUS instrument is essentially a fully functional SIMS instrument with an additional molecule-filtering detector, the SSAMS. The combination of these two techniques mitigates the drawbacks of each and enables new measurement paradigms for SIMS-like microanalysis. Highlighted capabilities include molecule-free raster ion imaging for direct spatially resolved analysis of heterogeneous materials with or without perturbed isotopic compositions. The NAUTILUS' sensitivity to trace elements is at least 10× better than commercial SIMS instruments due to near-zero background conditions. We describe the design and construction of the NAUTILUS, and its performance applied to topics in nuclear materials analysis, cosmochemistry, and geochemistry.