We present the first spectroscopic measurements of the ATLAS and Aliqa Uma streams from the Southern Stellar Stream Spectroscopic Survey (S5), in combination with the photometric data from the Dark Energy Survey and astrometric data from Gaia. From the coherence of spectroscopic members in radial velocity and proper motion, we find that these two systems are extremely likely to be one stream with discontinuity in morphology and density on the sky (the "kink" feature). We refer to this entire stream as the ATLAS-Aliqa Uma stream, or the AAU stream. We perform a comprehensive exploration of the effect of baryonic substructures and find that only an encounter with the Sagittarius dwarf ~0.5Gyr ago can create a feature similar to the observed "kink." In addition, we also identify two gaps in the ATLAS component associated with the broadening in the stream width (the "broadening" feature). These gaps have likely been created by small mass perturbers, such as dark matter halos, as the AAU stream is the most distant cold stream known with severe variations in both the stream surface density and the stream track on the sky. With the stream track, stream distance, and kinematic information, we determine the orbit of the AAU stream and find that it has been affected by the Large Magellanic Cloud, resulting in a misalignment between the proper motion and stream track. Together with the Orphan-Chenab Stream, AAU is the second stream pair that has been found to be a single stream separated into two segments by external perturbation.